U.S. patent number 10,253,337 [Application Number 15/830,659] was granted by the patent office on 2019-04-09 for recombinant yeast and use thereof.
This patent grant is currently assigned to Stellenbosch University. The grantee listed for this patent is Stellenbosch University. Invention is credited to Rosemary Anne Cripwell, Shaunita Hellouise Rose, Willem Heber Van Zyl.
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United States Patent |
10,253,337 |
Cripwell , et al. |
April 9, 2019 |
Recombinant yeast and use thereof
Abstract
A recombinant yeast that expresses both an .alpha.-amylase (SEQ
ID NO: 1) and a glucoamylase (SEQ ID NO: 2) from Talaromyces
emersonii (recently re-named as Rasamsonia emersonii) is provided.
The use of the recombinant yeast in a process for producing an
alcohol, in particular a biofuel, from starch or sugars is also
described.
Inventors: |
Cripwell; Rosemary Anne
(Stellenbosch, ZA), Van Zyl; Willem Heber
(Stellenbosch, ZA), Rose; Shaunita Hellouise
(Somerset West, ZA) |
Applicant: |
Name |
City |
State |
Country |
Type |
Stellenbosch University |
Stellenbosch |
N/A |
ZA |
|
|
Assignee: |
Stellenbosch University
(Stellenbosch, ZA)
|
Family
ID: |
58159833 |
Appl.
No.: |
15/830,659 |
Filed: |
December 4, 2017 |
Prior Publication Data
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|
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Document
Identifier |
Publication Date |
|
US 20180155744 A1 |
Jun 7, 2018 |
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Foreign Application Priority Data
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|
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Dec 5, 2016 [GB] |
|
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1620658.3 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12Y
302/01001 (20130101); C12N 9/242 (20130101); C12P
7/06 (20130101); C12Y 302/01 (20130101); C12P
7/16 (20130101); C12N 9/2405 (20130101); Y02E
50/10 (20130101) |
Current International
Class: |
C12P
7/06 (20060101); C12N 9/24 (20060101); C12N
9/30 (20060101); C12N 15/10 (20060101); C12N
9/26 (20060101); C12P 7/16 (20060101) |
References Cited
[Referenced By]
U.S. Patent Documents
Foreign Patent Documents
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44 25 058 |
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Jan 1996 |
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DE |
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0 257 115 |
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Aug 1986 |
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EP |
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3 091 070 |
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Nov 2016 |
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EP |
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99/28448 |
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Jun 1999 |
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WO |
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2006/066579 |
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Jun 2006 |
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WO |
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2007/057018 |
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May 2007 |
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WO |
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108941 |
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Sep 2009 |
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WO |
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03/016524 |
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Feb 2013 |
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WO |
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2014/058572 |
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Apr 2014 |
|
WO |
|
Other References
Van Zyl et al., Applied Microbiology and Biotechnology, Sep. 2012,
95(6), 1377-1388. cited by examiner.
|
Primary Examiner: Monshipouri; Maryam
Attorney, Agent or Firm: McNeill Baur PLLC
Claims
The invention claimed is:
1. A recombinant yeast which has been transformed with: a) a first
heterologous gene which encodes an .alpha.-amylase from Rasamsonia
emersonii having .alpha.-amylase activity, the first heterologous
gene consisting of an amino acid sequence which is at least 90%
identical to SEQ ID NO: 1 and which has a starch-binding domain,
wherein the nucleic acid sequence of the first gene is not
codon-optimized; and b) a second heterologous gene which encodes a
glucoamylase from Rasamsonia emersonii having glucoamylase
activity, the second heterologous gene consisting of an amino acid
sequence which is at least 90% identical to SEQ ID NO: 2 and which
has a starch-binding domain, wherein the nucleic acid sequence of
the second gene is optionally codon-optimized; the recombinant
yeast being capable of converting raw and cooked starch to ethanol
in a single step without the addition of exogenous starch
hydrolysing enzymes.
2. The recombinant yeast according to claim 1, wherein the amino
acid sequence of the .alpha.-amylase is SEQ ID NO: 1.
3. The recombinant yeast according to claim 1, wherein the amino
acid sequence of the glucoamylase is SEQ ID NO: 2.
4. The recombinant yeast according to claim 1, wherein the nucleic
acid sequence of the first gene is at least 85% identical to SEQ ID
NO: 3.
5. The recombinant yeast according to claim 1, wherein the nucleic
acid sequence of the second gene is: (a) codon-optimized and is at
least 85% identical to SEQ ID NO: 4; or (b) not codon-optimized and
is at least 85% identical to SEQ ID NO: 5.
6. The recombinant yeast according to claim 1, wherein the yeast is
a Saccharomyces species.
7. The recombinant yeast according to claim 6, wherein the yeast is
a Saccharomyces cerevisiae species.
8. A process for producing an alcohol from starch or sugars, the
process comprising the steps of: a) adding the recombinant yeast
according to claim 1 to a composition comprising starch or sugars;
b) causing the recombinant yeast to express and secrete (i) an
.alpha.-amylase from Rasamsonia emersonii consisting of an amino
acid sequence which is at least 90% identical to SEQ ID NO: 1 and
(ii) a glucoamylase from Rasamsonia emersonii consisting of an
amino acid sequence which is at least 90% identical to SEQ ID NO:
2; c) causing saccharification and/or fermentation to occur so that
the starch or sugars are converted to an alcohol in a single
step.
9. The process according to claim 8, wherein the starch is grain
starch.
10. The process according to claim 8, wherein the starch is raw
starch.
11. The process according to claim 10, wherein the raw starch is
hydrolysed by the recombinant yeast without requiring cooking of
the starch.
12. The process according to claim 11, wherein the raw starch is
hydrolysed by the recombinant yeast at a temperature of no more
than 40.degree. C.
13. The process according to claim 8, wherein the sugars comprise
glucose.
14. The process according to claim 8, wherein the alcohol is
selected from the group consisting of ethanol and butanol.
15. The process according to claim 14, wherein the alcohol is
ethanol.
16. The A process according to claim 8, wherein enzymes exogenous
to the recombinant yeast are also added to the composition.
17. The process according to claim 16, wherein the exogenous
enzymes are added in an amount which is at least 50% less than the
amount of enzymes added to cold hydrolysis processes which do not
use the recombinant yeast of claim 1.
18. The recombinant yeast of claim 1, which is further capable of
attaining a carbon conversion of greater than 70% when the starch
is corn starch.
19. The process of claim 8, which attains a carbon conversion of
greater than 70%.
Description
CROSS-REFERENCE TO RELATED APPLICATION
This application claims the benefit of priority of United Kingdom
Application No. GB 1 620 658.3, filed Dec. 5, 2016, which is
incorporated by reference herein in its entirety for any
purpose.
SEQUENCE LISTING
The present application is filed with a Sequence Listing in
electronic format. The Sequence Listing is provided as a file
entitled "2017-12-04_01204-0001-00US_P3338US_ST25.txt" created on
Nov. 27, 2017, which is 34,663 bytes in size. The information in
the electronic format of the sequence listing is incorporated
herein by reference in its entirety.
FIELD OF THE INVENTION
The invention relates to a recombinant yeast for converting raw and
soluble starch to an alcohol such as ethanol, particularly for use
as a biofuel.
BACKGROUND TO THE INVENTION
Cost effective, renewable and sustainable energy is a global
concern, which has increased investigations into alternative fuel
sources. Starch-rich biomass together with sugarcane represents the
main substrates for bioethanol production (Bai et al., 2008). It is
produced by plants as an energy store and consists of .alpha.-1,4
linked glucose units with .alpha.-1,6 branching points. The amylose
and amylopectin polymers are densely packed in starch granules
forming a semi-crystalline structure with inter- and
intra-molecular bonds.
A combination of .alpha.-amylases and glucoamylases is required for
the complete hydrolysis of starch. Starch granules are insoluble in
cold water and are often resistant to enzymatic hydrolysis
(Uthumporn et al., 2010). The conventional process for the
conversion of starch to ethanol requires a heat intensive
liquefaction step to gelatinise the starch and thermostable
.alpha.-amylases, followed by saccharification with glucoamylases.
The high temperatures required for the initial processes usually
account for approximately 30-40% of the total energy required for
ethanol production (Szymanowska-Powalowska et al., 2012).
An alternative to this is a cold hydrolysis process at temperatures
below the onset of starch gelatinization (65.degree. C. for corn)
(Robertson et al., 2006). Benefits of this process include reduced
energy requirements and a higher nutritional content for the dried
distillers' grains with solubles (DDGS) (Nkomba et al., 2016). DDGS
are produced in large quantities during bioethanol production and
represent a valuable ingredient for livestock feed (Brehmer et al.,
2008).
Consolidated bioprocessing (CBP) combines enzyme production,
hydrolysis and fermentation into a one-step process for bioethanol
production at low temperatures. This technology represents a
promising alternative for the economic production of biofuel from
lignocellulosic and starchy feedstocks. CBP could simplify
operational processes (e.g. number of control steps and reaction
vessels) and therefore reduce maintenance and production costs. CBP
systems use a single organism that is able to produce the enzymes
required for hydrolysis of starch at low temperatures, i.e. cold
hydrolysis, as well as convert the resultant sugars to ethanol. The
cold process requires amylases that have the ability to digest raw
starch efficiently at fermentation conditions. A few raw starch
hydrolyzing amylases have been reported to date (Mamo and Gessesse,
1999; Robertson et al., 2006; Celi ska et al., 2015). These
amylases differ from conventional amylases in their affinity and
interaction with the microcrystalline structures of starch
granules. A starch binding domain (SBD) is a key characteristic of
these enzymes and enables them to bind effectively to the surface
of raw starch granules.
A comprehensive review on consolidated bioprocessing systems by
Salehi Jouzani and Taherzadeh (2015) highlighted different CBP
strategies, diversity in substrate types and the organisms involved
in fermenting the sugars. One of the main challenges remains the
simultaneous production of the amylases with high substrate
affinities and specific activity (den Haan et al., 2013). In
addition, fermentation requirements are ethanol concentrations in
excess of 10-12% (wv.sup.-1) within 48 to 72 hours (Bothast and
Schlicher, 2005). For example, raw starch amylase encoding genes
from Lipomyces kononenkoae and Saccharomycopsis fibuligera (Eksteen
et al., 2003; Knox et al., 2004), Rhizopus arrhizus (Yang et al.,
2011), Aspergillus tubingensis (Viktor et al., 2013) and
Thermomyces lanuginoses and S. fibuligera or L. kononenkoae (LKA1)
protein (U.S. Pat. No. 9,243,256) have been expressed in
Saccharomyces cerevisiae, a yeast which is an efficient ethanol
producer but which on its own lacks the ability to degrade
starch.
However, none of these transformed yeasts produce sufficient
amounts of amylase to support efficient conversion of raw starch to
ethanol in a single step at commercial scale. Although a
bioengineered S. cerevisiae strain that secretes a glucoamylase is
commercially available (TransFerm.RTM. from Lallemand
(www.ethanoltech.com/transferm)), it lacks the required
.alpha.-amylase enzymes for starch liquefaction (den Haan et al.,
2015) and is therefore only a semi-CBP yeast. The TransFerm.RTM.
yeast strain is thus only suitable for the conventional (warm)
process, as it only consolidates the saccharification and
fermentation processes after starch liquefaction. CBP has therefore
not yet been implemented on a commercial level, with the main
challenge being the availability of a microorganism that can
express suitable enzymes and have a high fermentation capacity.
Other cold simultaneous saccharification and fermentation (SSF)
processes have been developed for ethanol production from starchy
substrates (Balcerek and Pielech-Przybylska, 2013;
Szymanowska-Powalowska et al., 2014; Nkomba et al., 2016). In these
processes, granular starch hydrolyzing enzyme (GSHE) cocktails are
added to the feedstock in addition to the yeast. Genencor's STARGEN
001.TM. and STARGEN 002.TM. cocktails (Dupont-Danisco, Itasca,
Itasca) hydrolyse raw starch at low temperatures (48.degree. C.
recommended for SSF), while POET (Sioux Falls, South Dekota, USA)
uses a patented blend of Novozymes enzymes (POET BPX technology) in
an SSF process (Gorgens et al., 2015). However, these cold starch
hydrolysis processes require high enzyme loadings and the cost of
the commercial enzymes, e.g. STARGEN.TM. (Genencor International,
California, USA), is high.
There thus remains a need for a yeast which can be used in a CBP
process for producing ethanol from raw starch, without requiring
the addition of amylases from a source other than the yeast.
SUMMARY OF THE INVENTION
According to a first embodiment of the invention, there is provided
a recombinant yeast which has been transformed with: a) a first
heterologous gene which encodes an .alpha.-amylase comprising an
amino acid sequence which is at least 70% identical to SEQ ID NO:
1, wherein the nucleic acid sequence of the first gene is not
codon-optimized; and b) a second heterologous gene which encodes a
glucoamylase comprising an amino acid sequence which is at least
70% identical to SEQ ID NO: 2, wherein the nucleic acid sequence of
the second gene is optionally codon-optimized.
The amino acid sequence of the .alpha.-amylase may be at least 80%
identical to SEQ ID NO: 1; the amino acid sequence of the
.alpha.-amylase may be at least 90% identical to SEQ ID NO: 1; or
the amino acid sequence of the .alpha.-amylase may be identical to
SEQ ID NO: 1.
The amino acid sequence of the glucoamylase may be at least 80%
identical to SEQ ID NO: 2; the amino acid sequence of the
glucoamylase may be at least 90% identical to SEQ ID NO: 2; or the
amino acid sequence of the glucoamylase may be identical to SEQ ID
NO: 2.
The nucleic acid sequence of the first heterologous gene may be at
least 70% identical to SEQ ID NO: 3, at least 80% identical to SEQ
ID NO: 3, at least 90% identical to SEQ ID NO: 3, or may be
identical to SEQ ID NO: 3.
The nucleic acid sequence of the second heterologous gene may be at
least 70% identical to either of SEQ ID NOS: 4 and 5, depending on
whether the sequence has been codon-optimized or not; and may be at
least 80% identical to either of SEQ ID NOS: 4 and 5, at least 90%
identical to either of SEQ ID NOS: 4 and 5, or may be identical to
either of SEQ ID NOS: 4 and 5.
The yeast may be a Saccharomyces species, such as Saccharomyces
cerevisiae.
The yeast may be a yeast which is capable of converting sugars such
as glucose to alcohol.
The alcohol may be butanol or ethanol, and in particular is
ethanol.
The recombinant yeast may be capable of hydrolyzing raw starch in
the absence of enzymes from a source other than the recombinant
yeast. The raw starch may be hydrolysed at a temperature of about
40.degree. C. or lower.
According to a second embodiment of the invention, there is
provided a process for producing an alcohol from sugars, the
process comprising the step of using a recombinant yeast as
described above to convert the sugars to alcohol.
The sugars may comprise glucose.
The alcohol may be ethanol or butanol, and is typically
ethanol.
According to a third embodiment of the invention, there is provided
a process for producing an alcohol from starch, the process
comprising the step of using a recombinant yeast as described above
to convert the starch to alcohol.
The recombinant yeast may be added to a composition comprising
starch or sugars, and may be allowed to express and secrete (i) an
.alpha.-amylase comprising an amino acid sequence which is at least
70% identical to SEQ ID NO: 1 and (ii) a glucoamylase comprising an
amino acid sequence which is at least 70% identical to SEQ ID NO:
2, so that saccharification and/or fermentation of the starch
and/or sugars occurs so as to produce an alcohol.
The starch may be a grain starch.
The starch may be raw (granular) starch or may be soluble (cooked)
starch.
The raw starch may be hydrolysed by the recombinant yeast without
requiring cooking of the starch. For example, the raw starch may be
hydrolysed by the recombinant yeast at a temperature of about
40.degree. C. or lower.
The alcohol may be ethanol or butanol, and is typically
ethanol.
The process may be a Consolidated Bioprocessing (CBP) process for
producing a biofuel.
Enzymes exogenous to the recombinant yeast may also be added to the
composition. The exogenous enzymes may be added in an amount which
is at least 50% less than the amount of enzymes added to cold
hydrolysis processes which do not use the recombinant yeast of the
invention.
According to a further embodiment of the invention, there is
provided the use of a recombinant yeast as described above in a
method of producing an alcohol from starch or sugars.
The alcohol may be a biofuel.
BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 Schematic representation of the vector constructs used in
example 1. Amylase encoding genes were amplified using PCR and
respectively cloned onto the yBBH1 and yBBH4 vectors (a, b and c).
The ENO1.sub.P-.alpha.-amylases-ENO1.sub.T cassettes were cloned
onto the yBBH1-glucoamylase plasmids (d), to enable co-expression
of the genes. BamHI and BglII restriction enzyme sites were used
for yeast mediated ligation (YML).
FIG. 2 Extracellular .alpha.-amylase activity displayed by the S.
cerevisiae Y294 strains expressing the (a) ateA, amyA, (b) apuA and
(c) temA gene derivatives, respectively. The S. cerevisiae
Y294[AmyA] strain was used for benchmark .alpha.-amylase
production. Values represent the mean of three repeats and error
bars represent the standard deviation. Supernatant from the S.
cerevisiae Y294 strains (after 72 hours) was subjected to SDS-PAGE
followed by silver staining. The arrows indicate the presence of
the recombinant (d) AmyA, AteA, (e) ApuA and (f) TemA protein
species, respectively. The S. cerevisiae Y294[BBH1] strain was used
as the reference strain and the protein size marker (M) is depicted
on the left hand side.
FIG. 3 Extracellular glucoamylase activity displayed by the S.
cerevisiae Y294 strains expressing the (a) ateG and (b) temG gene
derivatives, respectively. The S. cerevisiae Y294[GlaA] strain was
used for benchmark glucoamylase production. Values represent the
mean of three repeats and error bars represent the standard
deviation. Supernatant from the S. cerevisiae Y294 strains (after
72 hours) was subjected to SDS-PAGE followed by silver staining.
The arrows indicate the presence of the recombinant (c) AteG and
(d) TemG protein species, respectively. The S. cerevisiae
Y294[BBH1] strain was used as the reference strain and the protein
size marker (M) is depicted on the left hand side.
FIG. 4 The amylolytic S. cerevisiae Y294 strains were evaluated on
200 gl.sup.-1 raw corn starch and 5 gl.sup.-1 glucose as sole
carbohydrate source. The (a and b) ethanol and (c and d) glucose
production was monitored overtime. Results from the best performing
strains (left panel) and suboptimal strains (right panel) came from
the same fermentation. Values represent the mean of three repeats
and error bars represent the standard deviation.
FIG. 5 The performance of S. cerevisiae Y294[TemG_Opt-TemA_Nat] in
a 2 liter bioreactor. (a) Ethanol concentrations at 26.degree. C.
(-.circle-solid.-) and 30.degree. C. (-.box-solid.-) and residual
glucose concentrations at 26.degree. C. (-.largecircle.-) and at
30.degree. C. (-.quadrature.-) and (b) carbon conversion (%) at
26.degree. C. (-.circle-solid.-) and 30.degree. C. (-.box-solid.-),
respectively, with 2.times.SC.sup.-URA broth supplemented with 5
gl.sup.-1 glucose and 200 gl.sup.-1 raw corn starch. Values
represent the mean of triplicate repeats and error bars represent
the standard deviation.
FIG. 6 Schematic representation of the final vector and gene
cassettes used in this study. The TEF.sub.P-amdSYM-TEF.sub.T
cassette (a) was cloned onto yBBH1 to generate the yBBH1-amdSYM
expression vector. The ENO1 temA_Nat and temG_Opt gene cassettes
(b) were amplified using PCR and contained flanking regions
homologous to the .delta. integration sites.
FIG. 7 Comparison of industrial transformants after integration of
temA and temG gene cassettes. Ethanol produced (a) and carbon
conversion (%) (b) displayed by S. cerevisiae Ethanol Red.TM.
(-.quadrature.-) and M2n (-.diamond.-) parental strains and S.
cerevisiae Ethanol Red.TM. T1 (-.tangle-solidup.-), T12
(-.box-solid.-), M2n T1 (-.diamond-solid.-) and Mn2 T2
(-.circle-solid.-) amylolytic transformants at a fermentation
temperature of 30.degree. C. on 200 gl.sup.-1 raw corn starch.
SC-Ac (c) and SC-Acr (d) plate assays confirmed the ability of
recombinant S. cerevisiae Ethanol Red.TM. T12 and M2n T1 strains to
utilise acetamide and acrylamide, respectively, whereas the
parental S. cerevisiae Ethanol Red.TM. and M2n strains indicated no
growth.
FIG. 8 Comparison between the laboratory S. cerevisiae
Y294[TemG_Opt-TemA_Nat] strain (-.circle-solid.-) and the
industrial amylolytic S. cerevisiae Ethanol Red.TM. T12 strain at
30.degree. C. (-.box-solid.-) and 37.degree. C.
(-.tangle-solidup.-). The production of ethanol (a), glucose (b),
maltose (c) and glycerol (d) were compared using
2.times.SC.sup.-URA fermentation media that contained 5 gl.sup.-1
glucose and 200 gl.sup.-1 raw corn starch. Data are the mean of 3
repeats showing standard deviation.
FIG. 9 Different fermentation broth conditions during fermentation
at 37.degree. C. on 200 gl.sup.-1 raw corn starch. S. cerevisiae
Ethanol Red.TM. T12 in YP (-.diamond-solid.-), YP citrate-acid
buffer pH 5 (-.box-solid.-), SC citrate-acid buffer pH 5
(-.circle-solid.-) and SC citrate-acid buffer pH 5 with 10
gl.sup.-1 extra (NH.sub.4).sub.2SO.sub.4 (-.tangle-solidup.-).
Ethanol (a), glucose (b), glycerol concentrations (c) and carbon
conversion (percentage starch converted on a mol carbon basis) (d)
were compared. Data are the mean of 3 repeats showing standard
deviation.
FIG. 10 Ethanol concentrations produced by S. cerevisiae Ethanol
Red.TM. strains during fermentation with 200 gl.sup.-1 corn starch
at 30.degree. C. (a), at 37.degree. C., (b), carbon conversion
(percentage starch converted on a mol carbon basis) at 30.degree.
C. (c) and carbon conversion (percentage starch converted on a mol
carbon basis) at 37.degree. C. (d). Untransformed Ethanol
Red.TM.+28 .mu.l STARGEN.TM. (-.tangle-solidup.-), Ethanol Red.TM.
T12 (-.box-solid.-), Ethanol Red.TM. T12+2.8 .mu.l STARGEN.TM.
(-.diamond-solid.-), Ethanol Red.TM. T12+4.6 .mu.l STARGEN.TM.
(-.circle-solid.-) and Ethanol Red.TM. T12+14 .mu.l STARGEN.TM.
(--). Data are the mean of 3 repeats showing standard
deviation.
FIG. 11 Ethanol concentrations produced by S. cerevisiae M2n
strains during fermentation with 200 gl.sup.-1 at 30.degree. C.
(a), at 37.degree. C., (b), carbon conversion (percentage starch
converted on a mol carbon basis) at 30.degree. C. (c) and carbon
conversion (percentage starch converted on a mol carbon basis) at
37.degree. C. (d). The untransformed S. cerevisiae M2n strain+28
.mu.l STARGEN.TM. (-.tangle-solidup.-), M2n T1 (-.box-solid.-), M2n
T1+2.8 .mu.l STARGEN.TM. (-.diamond-solid.-) and M2n T1+4.6 .mu.l
STARGEN.TM. (-.circle-solid.-). Data are the mean of 3 repeats
showing standard deviation.
FIG. 12 Ethanol concentrations produced by recombinant industrial
S. cerevisiae strains during fermentation in YP media that
contained 5 gl.sup.-1 glucose and 200 gl.sup.-1 raw corn starch at
30.degree. C. Ethanol Red.TM. T12 (-.box-solid.-), M2n T1
(-.circle-solid.-) and M2n[TLG1-SFA1] (-.gradient.-).
FIG. 13 Performance of the S. cerevisiae Ethanol Red.TM. T12 strain
at different fermentation temperatures in YP media that contained 5
gl.sup.-1 glucose and 200 gl.sup.-1 raw corn starch. Ethanol
produced (a) and carbon conversion (%) (b) at 30.degree. C.
(-.diamond-solid.-), 34.degree. C. (-.circle-solid.-), 37.degree.
C. (-.box-solid.-) in a 5 liter bioreactor, and at 30.degree. C.
(--) in 100 ml serum bottles.
FIG. 14 Performance of the S. cerevisiae Ethanol Red.TM. T12 strain
during fermentation in YP media that contained 5 gl.sup.-1 glucose
and 200 gl.sup.-1 raw corn starch. Ethanol (a) and carbon
conversion (%) (b) at 30.degree. C. (total inoculum volume was 10%
(vv.sup.-1)). 10 ml Ethanol Red.TM. T12 (-.circle-solid.-), 10 ml
Ethanol Red.TM. T12+5 .mu.l commercial glucoamylase
(-.box-solid.-), 5 ml Ethanol Red.TM. T12+5 ml untransformed
Ethanol Red.TM. (--), 5 ml Ethanol Red.TM. T12+5 ml untransformed
Ethanol Red.TM.+5 .mu.l commercial glucoamylase
(-.diamond-solid.-).
FIG. 15 Ethanol concentrations produced by S. cerevisiae Ethanol
Red.TM. strains with different enzyme ratios at a fermentation
temperature of 30.degree. C. (total inoculum volume was 10%
(vv.sup.-1)). Untransformed Ethanol Red.TM.+28 .mu.l STARGEN.TM.
(-.tangle-solidup.-), Ethanol Red.TM. TemA_Nat+28 .mu.l STARGEN.TM.
(-.diamond-solid.-), Ethanol Red.TM. TemA_Nat+5 .mu.l
(-.circle-solid.-), 10 .mu.l (--) and 20 .mu.l (-.box-solid.-)
commercial glucoamylase, respectively, untransformed Ethanol
Red.TM.+10 .mu.l commercial glucoamylase (--) and 10 ml Ethanol
Red.TM. T12 (-.largecircle.-).
FIG. 16 SEQ ID NO: 1:--TemA protein. Protein sequence of Rasamsonia
emersonii alpha-amylase. [Rasamsonia emersonii CBS 393.64] Sequence
ID: GenBank no. XP_013324946.
FIG. 17 SEQ ID NO: 2:--TemG protein. Protein sequence of Rasamsonia
emersoni glucoamylase (secretion signal underlined). Sequence ID:
CAC28076.1.
FIG. 18 SEQ ID NO: 3:--temA_Nat gene. Synthetic DNA sequence coding
for the Rasamsonia emersoni alpha-amylase (putative secretion
signal underlined) used to produce TemA_Nat. This is 99% identical
to Rasamsonia emersonii CBS 393.64 alpha-amylase mRNA NCBI
Reference Sequence: Genbank no. XM_013469492 (1 nucleotide was
changed, compared to the original GenBank sequence, without
affecting the protein sequence).
FIG. 19 SEQ ID NO: 4: temG_Opt. DNA sequence coding for the
Rasamsonia emersonii glucoamylase (putative secretion signal
underlined), optimized for expression in S. cerevisiae (by
GenScript, USA).
FIG. 20 SEQ ID NO: 5: temG_Nat gene. Adapted native DNA sequence
coding for the Rasamsonia emersonii glucoamylase (TemG_Nat). This
sequence contained 3 nucleotide changes (bold and underlined)
compared to the original GenBank sequence (introns removed) and the
protein sequence is TemG.
FIG. 21 SEQ ID NO: 6 temA--original Genbank sequence for native
Rasamsonia emersonii CBS 393.64 Alpha-amylase mRNA NCBI Reference
Sequence: XM_013469492.1
FIG. 22 SEQ ID NO: 7: temG--original Talaromyces emersonii ga gene
for glucoamylase, exons 1-5 (Genbank sequence including introns;
GenBank: AJ304803.1).
DETAILED DESCRIPTION OF THE INVENTION
A recombinant yeast that expresses both an .alpha.-amylase and a
glucoamylase from Talaromyces emersonii (recently re-named as
Rasamsonia emersonii) is provided. The .alpha.-amylase comprising
an amino acid sequence which is at least 70% identical to SEQ ID
NO: 1 and the glucoamylase comprises an amino acid sequence which
is at least 70% identical to SEQ ID NO: 2. The recombinant yeast
can be used for converting starches and sugars to an alcohol, in
particular for use as a biofuel.
The amino acid sequence of the .alpha.-amylase can be at least 80%
identical to SEQ ID NO: 1. The amino acid sequence of the
.alpha.-amylase can also at least 90% identical to SEQ ID NO: 1; or
the amino acid sequence of the .alpha.-amylase can also be
identical to SEQ ID NO: 1.
The amino acid sequence of the glucoamylase can be at least 80%
identical to SEQ ID NO: 2; the amino acid sequence of the
glucoamylase can be at least 90% identical to SEQ ID NO: 2; or the
amino acid sequence of the glucoamylase can be identical to SEQ ID
NO: 2.
The yeast can be transformed with the native genes for both of
these enzymes or with a codon-optimized gene for the glucoamylase.
Nucleotide changes may also be made to the native gene so as to
disrupt restriction sites for cloning purposes, but without
altering the protein sequence (for example, as shown in FIGS. 19
and 20).
The nucleic acid sequence of the first heterologous gene can be at
least 70% identical to SEQ ID NO: 3, at least 80% identical to SEQ
ID NO: 3, at least 90% identical to SEQ ID NO: 3, or can be
identical to SEQ ID NO: 3.
In one embodiment, the yeast is transformed with a codon-optimized
gene for the glucoamylase, which has 69% identity to the native
sequence. In this embodiment, the yeast is transformed with a
glucoamylase which comprises a nucleic acid sequence which is at
least 68% similar to, at least 70% similar to, at least 80% similar
to, at least 90% similar to, or identical to SEQ ID NO: 4.
In another embodiment, instead of the yeast being transformed with
the codon-optimized glucoamylase, it can be transformed with a
non-codon-optimized glucoamylase comprising a nucleic acid sequence
which is at least 70% similar to, at least 80% similar to, at least
90% similar to, or identical to SEQ ID NO: 5.
The host yeast can be selected from those yeasts which are capable
of converting sugars to alcohol. Such sugars could be derived from
hydrolysed starch or other abundant hexose sugar-rich
feedstocks.
Exemplary yeasts for the present invention are Pichia (Hansenula)
spp. (e.g. P. anomala, P. capsulate and P. angusta (formerly H.
polymorpha)), Saccharomyces spp. (e.g. S. cerevisiae, S. italicus
and S. rouxii), Yarrowia (e.g. Y. lipolytica), Kluyveromyces spp.
(e.g. K. fragilis and K. lactis), Candida spp. (e.g. C.
tropicales), Torulopsis spp., Torulaspora spp., Schizosaccharomyces
spp. (e.g S. pombe), Citeromyces spp., Pachysolen spp., Debaromyces
spp., Metschunikowia spp., Rhodosporidium spp., Leucosporidium
spp., Botryoascus spp., Sporidiobolus spp., Endomycopsis spp.,
Schwanniomyces spp. (e.g. S. occidentalis) and the like.
In one embodiment, the yeast is a Saccharomyces species, and in
particular, Saccharomyces cerevisiae.
The yeast can be an industrial yeast, i.e. one that has been
developed for the industrial ethanol industry. Such yeasts
typically have one or more of the following properties: high
ethanol tolerance, fast acting, high alcohol yields, high cell
viability during fermentation, activity under a wide range of
fermentation conditions, etc. One example of such a yeast is
Ethanol Red.TM. from Fermentis (www.fermentis.com). Another example
is the S. cerevisiae M2n strain, which is a South African
distillery yeast. However, it will be apparent to a person skilled
in the art that other industrial yeasts could also be used.
The yeast is typically transformed without integration of any
antibiotic resistance gene (i.e. markerless integration).
Optionally, multiple copies of the .alpha.-amylase or glucoamylase
can be integrated into the genome of the yeast, e.g. the yeast can
be transformed with two or three copies of the .alpha.-amylase
and/or two or three copies of the glucoamylase. In one particular
embodiment, the recombinant strain contains one copy of the gene
encoding the .alpha.-amylase and two copies of the gene encoding
the glucoamylase.
The recombinant yeast can hydrolyse raw starch without requiring
the use of additional enzymes (e.g. exogenous amylase). The raw
starch can be hydrolysed at a temperature of about 40.degree. C. or
lower, such as from ambient temperature to about 40.degree. C.
The recombinant yeast can be used in a single-step process for
producing an alcohol from a starch. This process can be for
producing a biofuel, but it can also be a process for manufacturing
an alcoholic beverage, such as a beer. The alcohol can be butanol
or ethanol. In one embodiment, the alcohol is ethanol.
As raw starch can be hydrolysed by the recombinant yeast, this can
be used as the substrate without the need for an initial
liquefaction step. However, soluble (or cooked) starch could also
be used as the initial substrate.
The recombinant yeast can also be used in a process for producing
an alcohol from sugars. The sugars can be derived from hydrolysed
starch, from other abundant hexose sugar-rich feedstocks (e.g.
sugarcane) or from cellulose-derived sugar streams (i.e. with the
addition of cellulase enzymes). The sugars may comprise
glucose.
Although the recombinant yeast of the invention is capable of
hydrolyzing raw starch in the absence of an exogenous amylase, in
some embodiments additional enzymes can be added to the
fermentation process so as to reduce the fermentation time and/or
increase the carbon conversion. These enzymes can be a
glucoamylase, an amyloglucosidase (E.C. 3.2.1.3), an
.alpha.-amylase, or a mixture thereof which can hydrolyse raw
starch. For example, a cocktail of enzymes (Aspergillus kawachii
.alpha.-amylase expressed in Trichoderma reesei and a glucoamylase
from T. reesei) is available under the brand name STARGEN.TM. from
Genencor International. As the recombinant yeast is able to
continually replenish the enzymes in the fermentation broth, when
exogenous enzymes are added to a cold fermentation process using
the recombinant yeast of the invention, they can be added in a
reduced amount compared to the dosage that would be required if a
different yeast was being used (e.g. the Transferm.TM. yeast from
Lallemand). For example, the exogenous enzymes can be added in an
amount which is about 50% to about 95% less than the dosage which
is used in commercial cold fermentation processes. In particular,
the applicant has found that the addition of exogenous enzymes in
combination with the recombinant amylolytic yeast of the invention
allowed for a 90% reduction in the enzyme dosage, compared to the
conventional simultaneous saccharification (SSF) process with
untransformed host strains.
The single step saccharification and fermentation process may be
performed at temperatures ranging from ambient (room) temperature
to about 40.degree. C. More particularly, the temperature can be
from about 30.degree. C. to about 37.degree. C.
Alpha-amylases and glucoamylases from Aspergillus terreus,
Aureobasidium pullulans, Chaetomium thermophilum, Humicola grisea,
Neosartorya fischeri, Rhizomucor pusillus, Talaromyces emersonii,
Talaromyces stipitatus and Thermomyces lanuginosus were screened
for activity on starch and compared to the S. cerevisiae Y294[AmyA]
and Y294[GlaA] benchmark strains, respectively (Viktor et al.,
2013). Thereafter, several different amylolytic S. cerevisiae Y294
strains (ATCC 201160) were constructed and compared to the S.
cerevisiae Y294[AmyA-GlaA] benchmark strain (Viktor et al., 2013)
for their ability to hydrolyse raw corn starch and ferment the
resulting glucose to ethanol at a high substrate loading (200
gl.sup.-1 raw corn starch).
A combination of a glucoamylase from T. emersonii (TemG (SEQ ID NO:
2)) and an .alpha.-amylase from T. emersonii (TemA (SEQ ID NO: 1))
was found to be the most efficient at hydrolyzing raw corn starch
at fermentation conditions. T. emersonii is a thermophilic fungus
that is industrially important and well recognised for its
production of glycoside hydrolases (GHs) with special enzymatic
properties, especially cellulases (Amore and Faraco, 2012; Wang et
al., 2014). However, few studies have investigated its starch
hydrolyzing enzymes. T. emersonii amylases have also not previously
been expressed in S. cerevisiae.
Further investigations showed that when these enzymes were
expressed in yeast, a combination of the codon-optimized
glucoamylase gene (temG_Opt (SEQ ID NO: 4)) and native
.alpha.-amylase gene (temA_Nat (SEQ ID NO: 3)) provided even better
results than when the native glucoamylase gene (temG_Nat (SEQ ID
NO: 5)) was used or when both genes had been codon optimized. For
example, the recombinant S. cerevisiae Y294[TemG_Opt-TemA_Nat]
strain expressing the codon-optimized glucoamylase and native
.alpha.-amylase from T. emersonii produced 51.7 gl.sup.-1 ethanol
from raw starch after 120 hours of fermentation compared to 33.1
gl.sup.-1 produced by the S. cerevisiae Y294[AmyA-GlaA] benchmark
strain. The S. cerevisiae Y294[TemG_Opt-TemA_Nat] strain displayed
an 85% carbon conversion after 192 hours, compared to the 54% by
the benchmark strain.
The codon-optimized T. emersonii glucoamylase gene (temG_Opt (SEQ
ID NO: 4)) and native T. emersonii .alpha.-amylase gene (temA_Nat
(SEQ ID NO: 3)) were then transformed into two commercially
available industrial S. cerevisiae strains, namely Ethanol Red.TM.
and the M2n (MH-1000) distillery yeast (Favaro et al., 2015).
Ethanol Red.TM. is one of the most widely used yeast strains for
first generation bioethanol production (Stovicek et al., 2015). Few
studies have engineered S. cerevisiae Ethanol Red.TM. for the
expression of gene cassettes or adapted it for desired
characteristics. Demeke et al. (2013b) developed a D-xylose
fermenting strain, Wallace-Salinas and Gorwa-Grauslund (2013)
developed a strain capable of growing and fermenting spruce
hydrolysate and Stovicek et al. (2015b) introduced a xylose
consumption pathway into Ethanol Red.TM.. To the applicant's
knowledge, this study is the first to engineer S. cerevisiae
Ethanol Red.TM. for the expression of both an .alpha.-amylase and
glucoamylase for efficient raw starch conversion.
Two .delta.-integration gene cassettes were constructed to allow
for the simultaneous multiple integration of the codon-optimized T.
emersonii glucoamylase gene (temG_Opt) and the native T. emersonii
.alpha.-amylase gene (temA_Nat) into the genomes of the yeasts. The
T. emersonii amylases were both constitutively expressed under the
control of the ENO1 promoter, using the .delta.-integration DNA
transformation system. The amylolytic industrial strains were
evaluated at high solids loadings and were able to ferment starch
to ethanol in a single step with ethanol yields close to the
theoretical maximum yield. After 192 hours at 30.degree. C., the S.
cerevisiae Ethanol Red.TM. T12 and M2n T1 strains (containing
integrated temA_Nat and temG_Opt gene cassettes) produced 86.45
gl.sup.-1 and 99.40 gl.sup.-1 ethanol, respectively, corresponding
to a carbon conversion of 83.98% and 95.56%, respectively. In a
5-liter bioreactor, the S. cerevisiae Ethanol Red.TM. T12 strain
produced 82.6 gl.sup.-1 ethanol at 37.degree. C. after 192 hours,
which corresponded to 79% of the theoretical ethanol yield.
The recombinant yeasts described herein can achieve a carbon
conversion of greater than 70% (w/w), preferably of greater than
80%, and even more preferably of 90% or greater. Theoretical
ethanol yields are greater than 90%. Importantly, it was also shown
that transforming the host yeast with the .alpha.-amylase and
glucoamylase genes does not impede the robustness of the host
strain.
Thus, the recombinant yeasts of the invention are better and more
efficient than known benchmark strains for producing alcohol from
raw starch, and are also robust and thermotolerant. The recombinant
yeasts are therefore promising candidates for use in simultaneous
saccharification and fermentation (SSF) or consolidated
bioprocessing (CBP) processes. They represent a novel alternative
for reducing or avoiding the enzyme dosage required for raw starch
hydrolysis, as well as being able to provide continuous amylolytic
activity for a continuous cold fermentations process. It is
therefore envisaged that the recombinant yeast strain of the
invention could be used in commercial hot (cooked starch) and cold
fermentation processes that are currently used by ethanol producers
(i.e. as a "drop in candidate").
It is also envisaged that the use of recombinant yeasts of the
present invention will yield more cost-effective ethanol production
from starchy feedstocks.
Glossary of Terms
As used herein, the singular forms "a", "an" and "the" include the
plural references unless the content clearly dictates otherwise.
Thus for example, reference to a composition containing "a
compound" includes a reference to a mixture of two or more
compounds. It should be noted that the term "or" is generally
employed in the sense including "and/or" unless the context
dictates otherwise.
The term "about" as used in relation to a numerical value means,
for example, within 50% (.+-.50%) of the numerical value,
preferably .+-.30%, +20%, +15%, +10%, +7%, +5%, or +1%. Where
necessary, the word "about" may be omitted from the definition of
the invention.
The term "comprising" means "including". Thus, for example, a
composition or polypeptide "comprising" X may consist exclusively
of X or may include one or more additional components. In some
embodiments, "comprising" means "including principally, but not
necessarily solely".
As used herein, "heterologous" in reference to a nucleic acid or
protein includes a molecule that has been manipulated by human
intervention so that it is located in a place other than the place
in which it is naturally found. For example, a nucleic acid
sequence from one organism (e.g. from one strain or species) may be
introduced into the genome of another organism (e.g. of another
strain or species). A heterologous protein includes, for example, a
protein expressed from a heterologous coding sequence or a protein
expressed from a recombinant gene in a cell that would not
naturally express the protein.
The terms "polypeptide" and "protein" are used interchangeably.
The term "alpha-amylase" refers to the EC 3.2.1.1 class of enzymes
(1,4-alpha-D-glucan glucanohydrolase) which catalyse the hydrolysis
of alpha-1,4-glucosidic linkages. The enzymes are endo-hydrolases,
employ a retaining mechanism for hydrolysis (Enzyme Nomenclature,
1992) and belong to the glycoside hydrolase (GH) Family 13 and clan
GH-H (MacGregor et al., 2001). They hydrolyse the
1,4-alpha-D-glucosidic linkages in polysaccharides containing three
or more 1,4-alpha-linked D-glucose units. Hydrolysis reduces the
molecular size of starch and therefore the viscosity of the starch
solution. The alpha-amylases have considerably low sequence
similarity.
Glucoamylases (glucan .alpha.-1,4-glucosidase, EC 3.2.1.3) belong
to GH Family 15. Glucoamylases are exo-acting enzymes which
catalyse the hydrolysis of .alpha.-1,4- and .alpha.-1,6-glucosidic
linkages, thereby releasing the inverted .beta.-d-glucose from the
non-reducing ends of starch.
Further information of the structure and function of glucoamylases
and alpha-amylases may be found in Christiansen et al. FEBS Journal
276 (2009) 5006-5029.
The phrases "percent identity", "% identity," "protein identity",
"sequence identity" etc. as applied to polypeptide sequences, refer
to the percentage of identical residue matches between at least two
polypeptide sequences aligned using a standardized algorithm. Such
an algorithm may insert, in a standardized and reproducible way,
gaps in the sequences being compared in order to optimize alignment
between two sequences, and therefore achieve a more meaningful
comparison of the two sequences. Percent identity may be determined
using one or more computer algorithms or programs known in the art.
For example, the UWGCG Package provides the BESTFIT program which
can be used to calculate sequence identity (for example used on its
default settings) (Devereux et al. (1984) Nucleic Acids Research
12, p 387-395). The PILEUP and BLAST (Basic Local Alignment Search
Tool) algorithms can be used to calculate sequence identity or line
up sequences (typically on their default settings), for example as
described in Altschul S. F. (1993) J Mol Evol 36:290-300 and in
Altschul, S, F et al. (1990) J Mol Biol 215:403. Software for
performing BLAST analyses is available from several sources,
including the National Center for Biotechnology Information (NCBI),
Bethesda, Md., and on the internet at, for example,
"www.ncbi.nlm.nih.gov/". Preferably, the default settings of the
aforementioned algorithms/programs are used.
Whether an amino acid can be substituted at all (or deleted), or
whether it can only be substituted by a conserved amino acid can be
determined by comparing the amino acid sequence of one or more
members of the protein family. Amino acids that are identical in
all the members of a protein family often cannot be substituted.
Amino acids which are conserved can usually be substituted by other
conserved amino acids without significantly affecting the protein's
function. Amino acids which are not conserved within a family can
usually be freely substituted. Guidance in determining which amino
acid residues may be substituted, inserted, or deleted without
abolishing biological activity may also be found using computer
programs well known in the art, for example, LASERGENE software
(DNASTAR). Guidance concerning how to make phenotypically silent
amino acid substitutions is provided, for example, in J. U. Bowie
et al., "Deciphering the Message in Protein Sequences: Tolerance to
Amino Acid Substitutions," Science 247:1306-1310 (1990). Also, it
will be recognized by those skilled in the art that there may be
critical areas on the protein which determine activity, such as the
starch binding domain (SBD) and catalytic domain. The skilled
person will appreciate that it may be desirable to take into
account these areas when determining what changes to the amino acid
sequence can be made. A detailed overview of SBDs may be found in
Machovi and Jane , 2006. Amino acid residues essential to activity
of the polypeptide, and therefore preferably not subject to
alteration e.g. by substitution or deletion (or if substituted only
substituted by conservative substitutions), may be identified
according to procedures known in the art, such as site-directed
mutagenesis or alanine-scanning mutagenesis (see, e.g., Cunningham
and Wells, 1989, Science 244: 1081-1085). Sites of substrate-enzyme
interaction can also be determined by analysis of the
three-dimensional structure as determined by such techniques as
nuclear magnetic resonance analysis, crystallography or
photoaffinity labelling (see, e.g., de Vos et al., 1992, Science
255: 306-312; Smith et al., 1992, Journal of Molecular Biology 224:
899-904; Wlodaver et al., 1992, FEBS Letters 309: 59-64). Amino
acid deletions, substitutions or additions remote from an active or
binding site of a protein are generally more easily tolerated. In
general, it is often possible to replace residues which form the
tertiary structure, provided that residues performing a similar
function are used. In other instances, the type of residue may be
completely unimportant if the alteration occurs at a non-critical
region of the protein.
"Codon-optimization" refers to a well-known technique used to
improve heterologous protein secretion by increasing the
translational efficiency of the gene of interest. The redundancy of
the genetic code allows for numerous possibilities of DNA sequences
that can encode for the same protein. Foreign proteins are often
produced at low levels because wild-type foreign genes have not
evolved for optimum expression in alternative expression hosts. The
GC content and codon usage of genes are the two main sequence
features recognised to influence gene expression. In order to
efficiently express recombinant genes and secrete protein in higher
quantities, rare codons in the native gene are replaced with codons
that are more abundant in the genes of the host organism, without
changing the amino acid sequence of the protein itself. Codon
optimization techniques alter the codon usage pattern, which may
result in increased expression levels. Codon usage tables are
available, either to purchase or freely available (e.g.
www.kazusa.or.jp/codon and www.kazusa.or.jp/codon).
The term "starch" refers to any material comprised of the complex
polysaccharide carbohydrates of plant, comprised of amylose and
amylopectin with the formula (C6H10O5)x, wherein X can be any
number. In some embodiments, the starch-containing material may
comprise xylan. Examples of "starch-containing" material include
plant-based substrates (which may be fractionated plant material,
for example a cereal grain such as corn, which is fractionated into
components such as fiber, germ, protein and starch (endosperm)),
tubers, roots, stems, whole grains, grains, corms, cobs, tall
grasses, wheat, barley, rye, triticale, milo, sago, tapioca, rice
peas, beans, arrow root, cassava, sweet potatoes, cereals,
sugar-containing raw materials (e.g. molasses, fruit materials,
sugar cane or sugar beet), potatoes, cellulose-containing materials
(e.g. wood, wood residues, lignocelluloses, plant residues), wastes
from agriculture (e.g. corn stover, rice straw, cereal, bran,
damaged cereals, damaged potatoes, potato peel), non-cellulosic
feed stocks such as sorghum, municipal waste (e.g. newspaper, waste
paper), manure biomass, and agricultural residues etc.
The term "raw starch" refers to granular (unmodified) uncooked
starch that has not been subjected to gelatinization. At about
25.degree. C., starch granules start absorbing water, and as the
temperature increases, the granules start to vibrate vigorously.
Crystallinity decreases, and when the starch and water suspension
is heated above a critical point, designated the pasting or
gelatinization temperature, the granules disintegrate to make a
paste.
The term "hydrolysis of starch" refers to the chemical breakdown of
glycosidic bonds with the addition of water molecules.
The terms "liquefaction," "liquefy," "liquefact," and variations
thereof refer to the process or product of converting starch to
soluble dextrinized substrates (e.g. smaller polysaccharides).
Liquefact can also be referred to as "mash".
The term "gelatinization" refers to the alteration of the starch
granule from ordered, semi-crystalline granules to an amorphous
state and occurs in the presence of water. This is generally done
by heating the treated starch (typically treated with alpha
amylase) to temperatures up to 100.degree. C. The exact temperature
of gelatinization depends on the specific starch, and can readily
be determined by the skilled person.
The term "gelatinization temperature" refers to the lowest
temperature at which gelatinization of a starch containing
substrate begins.
The term "soluble starch" refers to starch resulting from the
hydrolysis of insoluble starch (e.g. granular/raw starch).
The terms "granular starch hydrolyzing (GSH) enzyme" and "enzymes
having granular starch hydrolyzing (GSH) activity" refer to enzymes
that are able to hydrolyse uncooked/granular starch.
The terms "saccharifying enzyme" and "starch hydrolyzing enzyme"
refer to any enzyme that is capable of converting starch to mono-
or oligosaccharides (e.g. a hexose or pentose).
The phrase "consolidated bioprocessing" refers to a one-step
process involving the use of a single organism that is able to
achieve liquefaction, hydrolysis and fermentation of starch in a
single fermentation vessel.
The phrase "simultaneous saccharification and fermentation (SSF)"
refers to a process in the production of end products in which a
fermenting organism, such as an ethanol producing microorganism and
at least one enzyme, such as a saccharifying enzyme, are combined
in the same process step in the same vessel.
"Exogenous enzymes" refers to enzymes which have not been expressed
by the recombinant yeast of the present invention.
Yeasts do not form an exact taxonomic or phylogenetic grouping, but
rather it is the colloquial name for single-celled members of the
fungal divisions Ascomycota and Basidiomycota. The budding yeasts
("true yeasts") are classified in the order Saccharomycetales. Most
reproduce asexually by budding, although a few do so by binary
fission. Yeasts are unicellular, although some species with yeast
forms may become multicellular through the formation of a string of
connected budding cells known as pseudohyphae, or false hyphae as
seen in most molds.
The invention will now be described in more detail by way of the
following non-limiting examples.
Example 1: Evaluation of .alpha.-Amylases and Glucoamylases and
Combinations Thereof for Raw Starch Hydrolysis
Materials and Methods
Media and Cultivation Conditions
All chemicals were of analytical grade and were obtained from Merck
(Darmstadt, Germany), unless otherwise stated. Escherichia coli
DH5.alpha. (Takara Bio Inc.) was used for vector propagation. The
E. coli transformants were selected for on Luria Bertani agar
(Sigma-Aldrich, Germany), containing 100 .mu.gml.sup.-1 ampicillin
and cultivated at 37.degree. C. in Terrific Broth (12 gl.sup.-1
tryptone, 24 gl.sup.-1 yeast extract, 4 mll.sup.-1 glycerol, 0.1 M
potassium phosphate buffer) containing 100 .mu.gml.sup.-1
ampicillin for selective pressure (Sambrook et al., 1989).
The S. cerevisiae Y294 strain was maintained on YPD plates (10
gl.sup.-1 yeast extract, 20 gl.sup.-1 peptone and 20 gl.sup.-1
glucose and 15 gl.sup.-1 agar) and amylolytic transformants were
selected and maintained on SC.sup.-URA plates (containing 6.7
gl.sup.-1 yeast nitrogen base without amino acids (BD-Diagnostic
Systems, Sparks, Md.), 20 gl.sup.-1 glucose, 1.5 gl.sup.-1 yeast
synthetic drop-out medium supplements (Sigma-Aldrich, Germany), 2%
corn starch (Sigma-Aldrich, Germany) and 15 gl.sup.-1 agar). The S.
cerevisiae strains were aerobically cultivated on a rotary shaker
(200 rpm) at 30.degree. C., in 125 ml Erlenmeyer flasks containing
20 ml double strength SC.sup.-URA medium (2.times.SC.sup.-URA
containing 13.4 gl.sup.-1 yeast nitrogen base without amino acids
(BD-Diagnostic Systems, Sparks, Md.), 20 gl.sup.-1 glucose and 3
gl.sup.-1 yeast synthetic drop-out medium supplements
(Sigma-Aldrich, Germany). All cultures were inoculated to a
concentration of 1.times.10.sup.6 cellsml.sup.-1.
Strains and Plasmids
The genotypes of the bacterial and fungal strains, as well as the
plasmids used in this example, are summarised in Table 1.
TABLE-US-00001 TABLE 1 Strains and plasmids used in this study
Strains and plasmids Genotype Reference E. coli DH5.alpha. supE44
.DELTA.lacU169 (.PHI.80lacZ.DELTA.M15) hsdR17 Sambrook et al. recA1
endA1 gyrA96 thi-1 relA1 (1989) S. cerevisiae strains Y294 .alpha.
leu2-3, 112 ura3-52 his3 trp1-289 ATCC 201160 Y294[BBH1] URA3
ENO1.sub.P-ENO1.sub.T Viktor et al. (2013) Y294[AmyA].sup.1 URA3
ENO1.sub.P-amyA-ENO1.sub.T Viktor et al. (2013) Y294[GlaA].sup.1
URA3 ENO1.sub.P-glaA-ENO1.sub.T Viktor et al. (2013)
Y294[AmyA-GlaA].sup.1 URA3 ENO1.sub.P-amyA-ENO1.sub.T; ENO1.sub.P-
Viktor et al. glaA-ENO1.sub.T (2013) Y294[ApuA_Nat].sup.1 URA3
ENO1.sub.P-apuA_Nat-ENO1.sub.T This study
Y294[ApuA_Opt-NatSS].sup.1 URA3
ENO1.sub.P-NatSS-apuA_Opt-ENO1.sub.T This study
Y294[ApuA_Nat-XYNSEC] URA3 ENO1.sub.P-XYNSEC-apuA_Nat- This
laboratory ENO1.sub.T Y294[ApuA_Opt-XYNSEC] URA3
ENO1.sub.P-XYNSEC-apuA_Opt- This study ENO1.sub.T
Y294[ApuA_Opt-OptXYNSEC] URA3 ENO1.sub.P-OptXYNSEC-apuA_Opt- This
study ENO1.sub.T Y294[AteA_Nat].sup.1 URA3
ENO1.sub.P-ateA_Nat-ENO1.sub.T This study Y294[TemA_Nat].sup.1 URA3
ENO1.sub.P-temA_Nat-ENO1.sub.T This study Y294[TemA_Opt] URA3
ENO1.sub.P-temA_Opt-ENO1.sub.T This study Y294[TemA_Opt-XYNSEC]
URA3 ENO1.sub.P-XYNSEC-temA_Opt- This study ENO1.sub.T
Y294[TemA_Nat- XYNSEC] URA3 ENO1.sub.P-XYNSEC-temA_Nat- This study
ENO1.sub.T Y294[TemA_Opt-NatSS].sup.1 URA3
ENO1.sub.P-NatSS-temA_Opt-ENO1.sub.T This study
Y294[AteG_Nat].sup.1 URA3 ENO1.sub.P-ateG_Nat-ENO1.sub.T This study
Y294[AteG_Nat-XYNSEC] URA3 ENO1.sub.P-XYNSEC-ateG_Nat- This study
ENO1.sub.T Y294[AteG_Opt-XYNSEC] URA3 ENO1.sub.P-XYNSEC-ateG_Opt-
This study ENO1.sub.T Y294[AteG_Opt-NatSS] URA3
ENO1.sub.P-NatSS-ateG_opt-ENO1.sub.T This study
Y294[TemG_Nat].sup.1 URA3 ENO1.sub.P-temG_Nat-ENO1.sub.T This study
Y294[TemG_Opt] URA3 ENO1.sub.P-temG_Opt-ENO1.sub.T This study
Y294[TemG_Opt-XYNSEC].sup.1 URA3 ENO1.sub.P-XYNSEC-temG_Opt- This
study ENO1.sub.T Y294[TemG_Nat-XYNSEC].sup.1 URA3
ENO1.sub.P-XYNSEC-temG_Nat- This study ENO1.sub.T
Y294[TemG_Opt-NatSS].sup.1 URA3
ENO1.sub.P-NatSS-temG_Opt-ENO1.sub.T This study Y294[TemG_Opt-AmyA]
URA3 ENO1.sub.P-temG_Opt-ENO1.sub.T; This study
ENO1.sub.P-amyA-ENO1.sub.T Y294[TemG_Opt-TemA_Nat] URA3
ENO1.sub.P-temG_Opt-ENO1.sub.T; This study
ENO1.sub.P-temA_Nat-ENO1.sub.T Y294[TemG_Opt-TemA_Opt] URA3
ENO1.sub.P-temG_Opt-ENO1.sub.T; This study
ENO1.sub.P-temA_Opt-ENO1.sub.T Y294[TemG_Opt-AteA_Nat] URA3
ENO1.sub.P-temG_Opt-ENO1.sub.T; This study
ENO1.sub.P-ateA_Nat-ENO1.sub.T Y294[TemG_Opt-ApuA_Nat] URA3
ENO1.sub.P-temG_Opt-ENO1.sub.T; This study
ENO1.sub.P-apuA_Nat-ENO1.sub.T Y294[GlaA_Nat-TemA_Nat] URA3
ENO1.sub.P-glaA-ENO1.sub.T; ENO1.sub.P- This study
temA_Nat-ENO1.sub.T Y294[TemG_Nat-AmyA] URA3
ENO1.sub.P-temG_Nat-ENO1.sub.T; This study
ENO1.sub.P-amyA-ENO1.sub.T Y294[TemG_Nat-AteA_Nat] URA3
ENO1.sub.P-temG_Nat-ENO1.sub.T; This study
ENO1.sub.P-ateA_Nat-ENO1.sub.T Y294[TemG_Nat-ApuA_Nat] URA3
ENO1.sub.P-temG_Nat-ENO1.sub.T; This study
ENO1.sub.P-apuA_Nat-ENO1.sub.T Y294[AteG_Nat-XYNSEC-AmyA] URA3
ENO1.sub.P-ateG_Nat-ENO1.sub.T; This study
ENO1.sub.P-amyA-ENO1.sub.T Plasmids yBBH1 bla URA3
ENO1.sub.P-ENO1.sub.T Njokweni et al. (2012) yBBH4 bla URA3
ENO1.sub.P-XYNSEC-ENO1.sub.T Njokweni et al. (2012) yBBH1-AmyA bla
URA3 ENO1.sub.P-amyA-ENO1.sub.T Viktor et al. (2013) yBBH1-GlaA bla
URA3 ENO1.sub.P-glaA-ENO1.sub.T Viktor et al. (2013) yBBH1-AteA_Nat
bla URA3 ENO1.sub.P-ateA_Nat-ENO1.sub.T This study yBBH1-ApuA_Nat
bla URA3 ENO1.sub.P-apuA_Nat-ENO1.sub.T This study yBBH1-TemA_Nat
bla URA3 ENO1.sub.P-temA_Nat-ENO1.sub.T This study yBBH1-TemA_Opt
bla URA3 ENO1.sub.P-temA_Opt-ENO1.sub.T This study
yBBH1-AteG_Nat-XYNSEC bla URA3 ENO1.sub.P-ateG_Nat-ENO1.sub.T This
study yBBH1-TemG_Nat bla URA3 ENO1.sub.P-temG_Nat-ENO1.sub.T This
study yBBH1-TemG_Opt bla URA3 ENO1.sub.P-temG_Opt-ENO1.sub.T This
study yBBH1-TemG_Nat-ApuA_Nat bla URA3
ENO1.sub.P-temG_Nat-ENO1.sub.T; This study
ENO1.sub.P-apuA_Nat-ENO1.sub.T yBBH1-TemG_Nat-AmyA bla URA3
ENO1.sub.P-temG_Nat-ENO1.sub.T; This study
ENO1.sub.P-amyA-ENO1.sub.T yBBH1-TemG_Nat-AteA_Nat bla URA3
ENO1.sub.P-temG_Nat-ENO1.sub.T; This study
ENO1.sub.P-ateA_Nat-ENO1.sub.T yBBH1-TemG_Opt-ApuA_Nat bla URA3
ENO1.sub.P-temG_Opt-ENO1.sub.T; This study
ENO1.sub.P-apuA_Nat-ENO1.sub.T yBBH1-TemG_Opt-AmyA bla URA3
ENO1.sub.P-temG_Opt-ENO1.sub.T; This study
ENO1.sub.P-amyA-ENO1.sub.T yBBH1-TemG_Opt-AteA_Nat bla URA3
ENO1.sub.P-temG_Opt-ENO1.sub.T; This study
ENO1.sub.P-ateA-ENO1.sub.T yBBH1-TemG_Opt-TemA_Nat bla URA3
ENO1.sub.P-temG_Opt-ENO1.sub.T; This study
ENO1.sub.P-temA_Nat-ENO1.sub.T yBBH1-TemG_Opt-TemA_Opt bla URA3
ENO1.sub.P-temG_Opt-ENO1.sub.T; This study
ENO1.sub.P-temA_Opt-ENO1.sub.T yBBH1-GlaA-TemA_Nat bla URA3
ENO1.sub.P-glaA-ENO1.sub.T; ENO1.sub.P- This study
temA_Nat-ENO1.sub.T yBBH4-AteG_Nat-XYNSEC-AmyA bla URA3
ENO1.sub.P-XYNSEC-ateG_Nat- This study ENO1.sub.T;
ENO1.sub.P-amyA-ENO1.sub.T .sup.1native secretion signal _Nat:
native coding sequence; _Opt: codon-optimized coding sequences
(GenScript); -NatSS: native secretion signal; -XYNSEC: native
secretion signal from Trichoderma reesei Xyn2 gene, -OptXYNSEC:
codon optimized-XYNSEC secretion signal
DNA Manipulations
Standard protocols were followed for all DNA manipulations and E.
coli transformations (Sambrook et al., 1989). All genes were
synthesised by GenScript (Piscataway, N.J., USA), based on the
nucleotide accession numbers listed below. The internal EcoRI,
XhoI, BamHI and BglII restriction sites were avoided, but the amino
acid sequence remained unaffected. The polymerase chain reaction
(PCR) was performed using a Perkin Elmer Gene Amp.RTM. PCR System
2400 and TaKaRa Ex Taq.TM. (Takara Bio Inc, Japan) as per the
manufacturer's recommendations. The amylase genes were amplified
using primers (Inqaba Biotec, South Africa) (Table 2) designed for
yeast mediated ligation (YML) and visualised on a 0.8% agarose gel.
DNA was eluted from agarose gels with the Zymoclean.TM. Gel
Recovery Kit (Zymo Research, USA).
The amylase genes were subcloned individually onto the yBBH1 or
yBBH4 plasmid (FIGS. 1a, b and c) in order to construct the
expression vectors listed in Table 1. The yBBH4 vector (FIG. 1c)
contained the sequence encoding for the XYNSEC secretion signal of
the Trichoderma reesei xyn2 (Den Haan et al., 2007) for directing
the secretion of the amylases. The
ENO1.sub.P-.alpha.-amylase-ENO1.sub.T cassettes were amplified from
the yBBH1-.alpha.-amylase vectors using YML cassette primers:
ENOCASS-L:
gtgcggtatttcacaccgcataggagatcgatcccaattaatgtgagttacctcactc (SEQ ID
NO: 35) and ENOCASS-R: cgggcctcttcgctattacgccagagcttagatct (SEQ ID
NO: 36) and cloned on the BglII site of yBBH1-glucoamylase or
yBBH4-glucoamylase vectors (FIGS. 1c and d). Sequence verification
of the final vector constructs was performed by the dideoxy chain
termination method, with an ABI PRISM.TM. 3100 Genetic Analyser
(CAF, Stellenbosch University).
TABLE-US-00002 TABLE 2 PCR oligo-primers used in this study with
the relevant restriction sites underlined (EcoRI = gaattc; NruI =
tcgcga; XhoI = ctcgag) Gene name SEQ (host ID Signal organism)
Sequence (5'-3') NO: peptide.sup.1 apuA ApuA_Nat-L:
tgcttatcaacacacaaacactaaatcaaagaattcatggcagccaactacgtttctcgattgttg
8 22 (A. ApuA_N-R:
gactagaaggcttaatcaaaagctctcgagtcacccctgccaagtattgctgaccgatgc 9
pullulans) ApuA_Opt-NatSS-L:
tctctacttgaccgggttggtgcagtgtttgactccagctcaatggagaagtcaatctat 10
ApuA_Opt-R:
ggactagaaggcttaatcaaaagctctcgagctaaccttgccatgtattggagactgagg 11
ApuA_optXynSec-L:
gaacccgtggctgtggagaagcgctcgcgattgactccagctcaatggagaagtc 12
ApuA_Opt-R:
ggactagaaggcttaatcaaaagctctcgagctaaccttgccatgtattggagactgagg 13
ateA AteA_Nat-L:
tgcttatcaacacacaaacactaaatcaaagaattcatgaagtggacctcctcgctcctcctctta
14 20 (A. AteA_Nat-R:
gactagaaggcttaatcaaaagctctcgagtcacctccaagtatcagcaactgtcaccgt 15
terreus) temA TemA_Nat-L:
tgcttatcaacacacaaacactaaatcaaagaattcatgacgcctttcgtcctcacggcc 16 19
(T. TemA_Nat-R
ggactagaaggcttaatcaaaagctctcgagctatctccatgtgtcgacaatcgtctccg 17
emersonii) TemA_Opt-NatOptSS-L:
tgcttatcaacacacaaacactaaatcaaagaattcatgacccdtttgttttgacagcc 18
TemA_Opt-R:
ggactagaaggcttaatcaaaagctctcgagctatctccaagtgtcaacaatagtttcag 19
TemA_Nat-xynsecSS-L:
gaacccgtggctgtggagaagcgctcgcgattgaccccggccgaatggcgcaaacaat 20
TemA_Opt-xynsecSS-L
gaacccgtggctgtggagaagcgctcgcgattgacaccagccgaatggagaaagcaatc 21
TemA_Opt-NatSS-L:
tcttgctggggaatgccgtgttggccttgacaccagccgaatggagaaagc 22 ateG
AteG_Nat-L:
tgcttatcaacacacaaacactaaatcaaagaattcatgacgcgcattctcaccctcgcccttcat
23 20 (A. AteG_Nat-R:
ggactagaaggcttaatcaaaagctctcgagctagcgccaagtggtgttcaccaccgcggt 24
terreus) AteG_Opt-NatSS-L:
gggctggctcttgtccaaagtgttgttggggcaccacaattggctcctagagcaactaca 25
AteG_Opt-R:
tggactagaaggcttaatcaaaagctctcgagctatctccaggttgtgttgacaacggcg 26
AteG_Nat-xynSS-L:
gaacccgtggctgtggagaagcgctcgcgagctccccaattggcccccagagcgacaacc 27
temG TemG_Nat-L:
tgcttatcaacacacaaacactaaatcaaagaattcatggcgtccctcgttgctggcgctctctgc
28 20 (T. TemG_Nat-R:
ggactagaaggcttaatcaaaagctctcgagtcactgccaactatcgtcaagaatggcggt 29
emersonii) TemG_Nat-xynsecSS-L:
gaacccgtggctgtggagaagcgctcgcgacgagcgcccgttgcagcgcgagccaccggt 30
TemG_Opt-xynsecSS-L:
gaacccgtggctgtggagaagcgctcgcgaagagccccagtcgcagccagagcaacaggt 31
TemG_Opt-R:
gactagaaggcttaatcaaaagctctcgagtcattgccaagagtcgtccaagattgcggt 32
TemG_Opt-NatOptSS-L:
ttatcaacacacaaacactaaatcaaagaattcatggcctccttagtcgcaggtgcctta 33
TemG_Opt-NatSS-L:
atcctgggcctgacgcctgctgcatttgcaagagccccagtcgcagccagagcaacaggt 34
.sup.1The length (amino acids) of putative signal peptides was
analysed using SignalP 4.1 (www.cbs.dtu.dk/services/SignalP).
Amylase Genes and GenBank Accession Numbers
The following amylases were cloned and expressed in S. cerevisiae
Y294. The native glucoamylases from A. pullulans (Accession no.
HM246718), A. terreus (Accession no. XP_001213553), H. grisea
(Accession no. M89475), T. emersonii (Accession no. AJ304803) and
T. lanuginosus (Accession no. EF545003), as well as the native
.alpha.-amylases from A. pullulans (Accession no. AEH03024), A.
terreus (Accession no. XM_001209405), N. fischeri (Accession no.
XP_001265628), R. pusillus (Accession no. AGJ52081) and T.
emersonii (Accession no. XM_013469492). Coding sequences for the
glucoamylases from C. thermophilum (Accession no. ABD96025), T.
stipitatus (Accession no. XP_002484948), A. terreus and T.
emersonii, as well for .alpha.-amylases from A. pullulans and T.
emersonii were codon-optimized for expression in S. cerevisiae
(GenScript, Piscataway, N.J., USA). T. emersonii has recently been
classified as Rasamsonia emersonii (Houbraken et al., 2012).
Yeast Transformations
The S. cerevisiae Y294 strain was grown overnight in 5 ml YPD broth
and prepared according to Cho et al. (1999). After electroporation,
1 ml of YPDS was immediately added to the cuvette. Cultures were
incubated at 30.degree. C. for 1 hour prior to plating out onto
SC.sup.-URA plates containing 2% starch. Plates were incubated at
30.degree. C. for 2-3 days and then transferred to 4.degree. C. for
24 hours to allow the starch to precipitate.
Activity Assays
For quantitative assays, yeast transformants were cultured in 20 ml
2.times.SC.sup.-URA medium in 125 ml Erlenmeyer flasks with
agitation at 200 rpm and sampling at 24 hour intervals. The
supernatant was harvested and extracellular enzymatic activity
levels were assessed colourimetrically (xMark.TM. Microplate
Spectrophotometer, Bio-Rad, San Francisco, USA) using the reducing
sugar assay with glucose as standard (Miller 1959). The
.alpha.-amylase activities were determined after a 5 minute
incubation with 0.2% soluble corn starch in 0.05 M citrate-acid
buffer (pH 5) at 37.degree. C.
Glucoamylase activity was determined by incubating 50 .mu.l
supernatant with 450 .mu.l of 0.2% soluble corn starch in 0.05 M
citrate-acid buffer (pH 5) at 37.degree. C. for 15 minutes. The
glucose concentration was determined using the D-Glucose Assay Kit
(Megazyme, Ireland) with absorbance measured at 510 nm (xMark.TM.
Microplate Spectrophotometer, Bio-Rad, San Francisco, USA).
Enzymatic activities were expressed as nano-katals per ml
(nkatml.sup.-1), with nkat defined as the enzyme activity needed to
produce 1 nmol of glucose per second under the described assay
conditions.
Protein Analysis
Recombinant S. cerevisiae Y294 strains were cultivated in 125 ml
Erlenmeyer flasks containing 20 ml 2.times.SC.sup.-URA medium for 3
days. Twenty microliters of supernatant was added to protein
loading buffer and the samples boiled for 3 minutes to denature the
proteins. The recombinant proteins were separated on an 8%
SDS-polyacrylamide gel using a 5% stacking gel and Tris-glycine
buffer (Sambrook et al., 1989). Electrophoresis was carried out at
100 V for .+-.90 minutes at ambient temperature and protein species
were visualised using the silver staining method (O'Connell and
Stults, 1997). The broad-range Page Ruler Prestained SM0671 Protein
Ladder (Fermentas, China) was used as a molecular mass marker.
Raw Starch Fermentations
Precultures were cultured in 60 ml 2.times.SC.sup.-URA media in 250
ml Erlenmeyer flasks and incubated at 30.degree. C. with agitation
of 200 rpm. Fermentations were performed with 2.times.SC.sup.-URA
media containing 200 gl.sup.-1 raw corn starch and 5 gl.sup.-1
glucose and inoculated with a 10% (vv.sup.-1) inoculum. Ampicillin
(100 .mu.gml.sup.-1) and streptomycin (50 .mu.gml.sup.-1) were
added to inhibit bacterial contamination. Agitation and incubation
were performed on a magnetic multi-stirrer at 30.degree. C., with
daily sampling through a syringe needle pierced through the rubber
stopper.
For bioreactor experiments with laboratory strains, precultures
were cultivated in 120 ml 2.times.SC.sup.-URA media in 500 ml
Erlenmeyer flasks at 30.degree. C. with agitation at 200 rpm.
Bioreactor fermentations were performed in a 2 liter MultiGen
Bioreactor (New Brunswick Scientific Corporation, Edison, N.J.)
containing 2.times.SC.sup.-URA media supplemented with 200
gl.sup.-1 raw corn starch and 5 gl.sup.-1 glucose as carbohydrate
source. A 10% (vv.sup.-1) inoculum was used in a total working
volume of 1 liter. Fermentations were carried out at 26.degree. C.
and 30.degree. C. with stirring at 300 rpm and daily sampling
through a designated sampling port. All fermentation experiments
were performed in triplicate.
High Performance Liquid Chromatography (HPLC) Analysis
Ethanol, glucose, maltose, glycerol and acetic acid concentrations
were quantified with HPLC using a Surveyor Plus liquid
chromatograph (Thermo Scientific) consisting of a liquid
chromatography pump, autosampler and refractive index (RI)
detector. The compounds were separated on a Rezex RHM
Monosaccharide 7.8.times.300 mm column (00H0132-K0, Phenomenex) at
80.degree. C. with 5 mM H.sub.2SO.sub.4 as mobile phase at a flow
rate of 0.6 mlmin.sup.-1.
Analytical Methods and Calculations
The theoretical CO.sub.2 concentrations were calculated according
to Favaro et al. (2015). The glucose equivalent is defined as the
mass of glucose resulting from the complete hydrolysis of starch,
i.e. 1.11 grams of glucose per gram of starch. The available carbon
(mol C in 100% hydrolysed substrate) was calculated based on the
available glucose equivalents and the carbon conversion is defined
as the percentage starch converted to fermentable products on a mol
carbon basis. This carbon conversion was calculated from ethanol,
glucose, maltose, glycerol, acetic acid and CO.sub.2
concentrations. The ethanol yield (% of the theoretical yield) was
calculated as the amount of ethanol produced per gram of consumed
glucose. The ethanol rate of productivity was calculated based on
ethanol titres produced per hour (gl.sup.-1h.sup.-1).
Statistical Analysis
Data was analysed using the Student's t-test.
Results
Functional Expression of Recombinant Amylases
The S. cerevisiae Y294 strain was used as host for the heterologous
gene expression of recombinant amylases. Recombinant strains were
constructed to express either an .alpha.-amylase or glucoamylase
encoding gene (Table 1) and evaluated for their ability to
hydrolyse corn starch using the S. cerevisiae Y294[AmyA] and
Y294[GlaA] strains, respectively, as benchmarks strains (Viktor et
al., 2013). All the recombinant strains evaluated in this study
were able to hydrolyse soluble starch (demonstrated by zones of
hydrolysis during plate assays--data not shown).
However, several amylase candidates showed significantly lower
levels of extracellular activity (nkatml.sup.-1), when compared to
the benchmark S. cerevisiae Y294 strains expressing the amyA and
glaA genes (data no shown). Thus, the following genes were omitted
from further evaluation: native glucoamylases from A. pullulans, H.
grisea and T. lanuginosus, as well as the codon-optimized
.alpha.-amylases from N. fischeri, R. pusillus and codon-optimized
glucoamylases from C. thermophilum and T. stipitatus. The different
gene variants for the ateA, apuA, temA, ateG and temG genes
contained different DNA sequences, but encoded for the same amino
acid sequence (for the mature protein).
.alpha.-Amylases
The ateA_Nat gene was efficiently expressed by the S. cerevisiae
Y294[AteA_Nat] strain, but the extracellular levels of activity
were consistently lower than that of the S. cerevisiae Y294[AmyA]
benchmark strain (FIG. 2a). Replacing the native secretion signal
with the native XYNSEC (S. cerevisiae Y294[AteA_Nat-XYNSEC]) did
not result in significant differences in either extracellular
activity or the amount of AteA secreted (FIGS. 2a and 2d). The
extracellular protein levels of AmyA and AteA were similar (FIG.
2d).
The S. cerevisiae Y294[ApuA_Nat] and Y294[TemA_Nat] strains
displayed more extracellular .alpha.-amylase activity on soluble
starch (FIGS. 2b and 2c) than the S. cerevisiae Y294[AmyA]
benchmark strain. Codon optimization of the apuA_Nat and temA_Nat
genes resulted in less extracellular activity due to a decrease in
enzyme concentration (FIGS. 2e and 2f). Changing the secretion
signal also resulted in a decrease in extracellular enzyme
concentration, with a negative impact on extracellular activity
(FIGS. 2c and 2d).
SDS-PAGE analysis of the supernatant indicated that most of these
.alpha.-amylases are glycosylated. ApuA and AteA protein species
(calculated molecular weights of 65.25 kDa and 64.14 kDa,
respectfully) (FIGS. 2b and 2d) are the least glycosylated with a
putative recombinant size of around 70 kDa, while TemA (calculated
molecular weight of 66.29 kDa) had a higher degree of glycosylation
(FIG. 2f) and a putative size of around 90 kDa. The large
heterogeneous smear between 110 and 150 kDa for the AmyA protein is
consistent with that of a previous report (Viktor et al.,
2013).
Glucoamylases
The replacement of the ateG_Nat secretion signal with the XYNSEC
sequence improved extracellular glucoamylase activity, albeit less
than the activity displayed by the S. cerevisiae Y294[GlaA] strain
(FIG. 3a). The S. cerevisiae Y294[AteG_Opt-XYNSEC] and
Y294[AteG_Nat-XYNSEC] strains produced similar levels of activity,
which exceeded the activity by the strains containing the native
ateG secretion signal. The S. cerevisiae Y294[AteG_Opt-NatSS]
strain secreted no visible protein (FIG. 3c) confirming that the
native ateG secretion signal negatively affected protein secretion.
Codon optimization did not have a visible effect on the
extracellular amount of AteG protein produced, despite the increase
in extracellular activity (FIGS. 3a and 3c).
A significant increase in extracellular glucoamylase activity was
observed when the temG gene sequence was codon-optimized (FIG. 3b).
At 72 hours, extracellular activity for the S. cerevisiae
Y294[TemG_Opt] strain was >3-fold higher than the S. cerevisiae
Y294[TemG_Nat] strain and >10-fold higher than the Y294[GlaA]
benchmark strain. Changing secretion signals for the expression of
the temG indicated that the optimized temG secretion signal
contributed to enhanced protein secretion and extracellular
activity (FIGS. 3b and 3d), whereas replacement with the XYNSEC
secretion signal had a negative impact.
SDS-PAGE analysis of the supernatant indicated that these
glucoamylases are glycosylated. The AteG protein species
(calculated molecular weight of 65.73 kDa) (FIG. 3c) had a putative
size of around 95 kDa, while the TemG protein (calculated molecular
weight of 63.57 kDa) is less glycosylated with a putative size of
around 85 kDa (FIG. 3d). Moreover, the intensity of the recombinant
protein species visualised using SDS-PAGE showed correlation with
the extracellular enzyme activity levels for all amylases.
Raw Corn Starch Fermentations
The amylase encoding genes that resulted in the highest levels of
extracellular activity when expressed in S. cerevisiae Y294
(apuA_Nat, ateA_Nat, temA_Nat, temA_Opt, ateG_Nat-XYNSEC, temG_Nat
and temG_Opt), together with the reference (amyA and glaA) genes,
were then used to construct amylolytic strains that produced an
.alpha.-amylase and glucoamylase combination (Table 1). The
recombinant yeast strains were evaluated for their ability to
hydrolyse raw starch and ferment glucose at a high substrate
loading under oxygen-limited conditions.
At 192 hours, the S. cerevisiae Y294[TemG_Opt-TemA_Nat] strain
produced the highest ethanol concentration (62.2 gl.sup.-1), which
is 59.7% of the theoretical value (FIG. 4a). After 120 hours, this
strain produced 51.7 gl.sup.-1 ethanol, which represents a 1.6-fold
improvement on the S. cerevisiae Y294[AmyA-GlaA] benchmark strain
(p=0.0013). Ethanol levels of 38.6 gl.sup.-1 and 39.4 gl.sup.-1
produced by the S. cerevisiae Y294[TemG_Opt-ApuA_Nat] and
Y294[TemG_Opt-AteA_Nat] strains, respectively, were also higher
than the benchmark strain (at 120 hours). The S. cerevisiae
Y294[TemG_Opt-TemA_Nat] strain accumulated 46.3 gl.sup.-1 residual
glucose after 192 hours of fermentation (FIG. 4c).
The S. cerevisiae Y294 strains expressing the TemG_Nat-AmyA,
TemG_Nat-AteA_Nat, TemG_Nat-ApuA_Nat and AteG_Nat-XYNSEC-AmyA
enzyme combinations produced less ethanol compared to the S.
cerevisiae Y294[AmyA-GlaA] benchmark strain (FIGS. 4a and 4b), with
little to no residual glucose detected (FIG. 4d). Overall, results
depicted in FIG. 4c indicated that the S. cerevisiae
Y294[TemG_Opt-TemA_Nat] strain was superior to the other strains
and this enzyme combination was effective in hydrolyzing raw corn
starch. At 192 hours, carbon conversion displayed by the S.
cerevisiae Y294[TemG_Opt-TemA_Nat] strain was 57% higher than that
displayed by the S. cerevisiae Y294[AmyA-GlaA] benchmark strain,
whereas the Y294[TemG_Opt-AteA_Nat] strain produced comparable
results to that of the benchmark strain (Table 3).
TABLE-US-00003 TABLE 3 Products formed by S. cerevisiae Y294
strains after 192 hours of fermentation at 30.degree. C. in 2
.times. SC.sup.-URA broth with glucose (5 g l.sup.-1) and raw corn
starch (200 g l.sup.-1) S. cerevisiae Y294 [TemG_Opt- [TemG_Opt-
[TemG_Opt- [TemG_Opt- [TemG_Opt- [GlaA- [GlaA-- Strains AmyA]
TemA_Nat] TemA_Opt] AteA_Nat] ApuA_Nat] AmyA] TemA_Nat] Substrate
(g l.sup.-1) Raw starch (dry 185 185 185 185 185 185 185 weight)
Glucose equivalent 208.5 208.5 208.5 208.5 208.5 208.5 208.5
Products (g l.sup.-1) Glucose 2.72 46.30 1.67 1.94 1.21 5.30 4.12
Glycerol 4.76 6.64 2.40 3.43 2.45 2.46 2.26 Maltose 1.09 1.03 1.07
1.14 0.95 1.02 1.17 Acetic acid 1.91 1.66 0.60 0.85 0.61 0.61 0.56
Ethanol 47.40 62.20 48.71 53.46 43.12 52.78 46.56 CO.sub.2.sup.1
45.33 59.50 46.59 51.13 41.25 50.48 44.53 Total 103.21 177.33
101.04 111.95 89.60 112.65 99.20 Carbon conversion 49.50 85.05
48.46 53.69 42.97 54.03 47.58 (%) Ethanol.sup.2 (% of 45.46 59.67
46.72 51.28 41.36 50.63 44.66 theoretical yield) Ethanol rate of
0.247 0.324 0.254 0.278 0.225 0.275 0.242 productivity.sup.3
.sup.1CO.sub.2 concentrations were deduced from the ethanol
produced .sup.2Ethanol yield (% of the theoretical yield) was
calculated as the amount of ethanol produced per gram of consumed
sugar (at a specific time point) .sup.3Ethanol rate of productivity
was calculated based ethanol titres produced per hour (g l.sup.-1
h.sup.-1)
The S. cerevisiae Y294[TemG_Opt-TemA_Nat] strain was evaluated in a
2 liter bioreactor (1 liter working volume) under two fermentation
temperatures (26.degree. C. and 30.degree. C.) (FIG. 5). After 192
hours, the final ethanol concentration (83.8 gl.sup.-1) was
significantly higher at a fermentation temperature of 26.degree. C.
(FIG. 4a), however the carbon conversion percentages were similar
(79-81%). After 192 hours, a decrease in fermentation temperature
resulted in 1.8-fold improvement in the ethanol concentration and
no residual glucose was detected at a fermentation temperature of
26.degree. C. (FIG. 4a). The carbon conversion displayed by the S.
cerevisiae Y294[TemG_Opt-TemA_Nat] strain (at 30.degree. C.) was
similar for both fermentation types (100 ml bottle fermentations
and bioreactor), 85% and 81% respectively, after 192 hours (FIGS.
4a and 5b).
Discussion
A selection of amylases from various fungi have been investigated
independently by several research groups, with raw starch
hydrolyzing enzymes being favoured for starch conversion to ethanol
(Robertson et al., 2006; Viktor et al., 2013; Favaro et al., 2015;
Celi ska et al., 2015). Approximately 10% of all amylases contain a
starch binding domain (SBD) (Sun et al., 2010), which is
classically associated with the adsorption of these enzymes to raw
starch granules, thereby enhancing the amylolytic rate and the
subsequent hydrolysis (Santiago et al., 2005; Mitsuiki et al.,
2005). Thus, for this study, the presence of a SBD was a
prerequisite when selecting amylases for expression in S.
cerevisiae.
Amylase genes were heterologously expressed in order to choose the
enzymes with the highest extracellular enzyme activity and to
investigate the effect of synonymous codon usage on gene expression
(Table 1). In this study, several amylase candidates showed
significantly low levels of extracellular activity, compared to the
benchmark strain (data not shown). Thus, the following genes were
omitted from further studies: native glucoamylases from A.
pullulans, H. grisea and T. lanuginosus, as well as the optimized
.alpha.-amylases from N. fischeri, R. pusillus and codon-optimized
glucoamylases from C. thermophilum and T. stipitatus.
High levels of protein expression can be correlated to the codon
adaptation index (CAI) (Carbone et al., 2003). A CAI value of 1.0
is considered to be ideal, while GenScript recommends that a CAI of
>0.8 is rated as good for expression in the desired expression
organism. Analysis of the genes' CAI values using GenScript's
OptimumGene.TM.
(www.genscript.com/cgi-bin/tools/rare_codon_analysis) indicated
that all CAI values increased when the genes were optimized.
GenScript's algorithm for gene optimization aims to improve gene
expression and therefore the synthetic amylase genes in this study
were codon-optimized for expression in S. cerevisiae. However,
results from this study indicated that increased gene expression
and protein secretion was not guaranteed by codon optimization
(FIGS. 2 and 3).
The strains expressing the apuA_Nat and temA_Nat genes were
superior to the strains expressing the codon-optimized counterparts
apuA_Opt-NatSS/apuA_Opt-OptXYNSEC and temA_Opt, respectively (FIGS.
2b and 2c), while optimization of the temG coding sequence resulted
in a significant increase in TemG_Opt protein secreted by the S.
cerevisiae Y294[TemG_Opt] strain (FIG. 3d). Increased recombinant
protein secretion correlated with enhanced levels of extracellular
activity, which suggested similar specific activities (FIGS. 2e and
2f) and SDS-PAGE analysis indicated that codon optimization did not
affect amylase protein size (FIGS. 2 and 3). Based on the deduced
amino acid sequences, the predicted molecular weights of the
unglycosylated amylases are around 64-70 kDa, which is in agreement
with previous reports on similar amylases (Gupta et al., 2003).
The temA_Nat had a CAI of 0.61 compared to temA_Opt with a CAI of
0.91. Surprisingly, however, the S. cerevisiae Y294[TemA_Nat]
strain produced 59% more extracellular .alpha.-amylase activity
than the S. cerevisiae Y294[TemA_Opt] strain after 72 hours. The
temG_Nat gene had a CAI of 0.58 compared to temG_Opt, which had a
CAI of 0.91. The extracellular glucoamylase activity for the S.
cerevisiae Y294[TemG_Nat] and Y294[TemG_Opt] strains represented a
>3-fold and 10-fold fold improvement, respectively, compared to
the S. cerevisiae Y294[GlaA] benchmark strain. Therefore, even for
genes originating from the same species (in this case T.
emersonii), significant differences in protein secretion and
extracellular enzyme activities were observed between native and
codon-optimized genes. Thus, CAI values alone cannot be relied upon
for improving gene expression.
The secretion of recombinant proteins into the culture medium
simplifies downstream purification methods (Damasceno et al.,
2012). Secretion signals are used to direct the propeptide to the
endoplasmic reticulum (ER) and then through the secretory pathway
(Futatsumori-Sugai and Tsumoto, 2010). Once in the ER, the mature
peptide is folded into its native structure and there are a number
of factors that effect this folding process (Tyo et al., 2012). The
secretion of recombinant proteins by yeast is a key industrial
objective for the biotechnology field, and significant efforts have
gone into improving protein secretion. This process is dependent on
the target protein, host strain and secretion signal sequence
(Hashimoto et al., 1998). Therefore, signal peptides represented an
important factor to consider when improving the concentration of
secreted protein.
The XYNSEC secretion signal from Trichoderma reesei's
.beta.-xylanase 2 gene has been used successfully for the secretion
of a number of proteins (van Wyk et al., 2010; van Rensburg et al.,
2012; Favaro et al., 2013) and was used in this study for
comparative purposes. All the native enzymes selected for this
study were successfully secreted using their native secretion
peptides, and the replacement of the native ateG signal peptide
encoding sequence with the XYNSEC sequence resulted in enhanced
extracellular activity (FIG. 3a). However, in general, the XYNSEC
secretion signal was less effective than the proteins' native
secretion signals.
Following the identification of successful amylase candidates,
novel gene combinations were expressed in S. cerevisiae Y294 in
order to obtain an amylolytic yeast suitable for raw starch CBP. It
was previously reported that starch fermentation by genetically
engineered strains is limited by the glucoamylase activity (Inlow
et al., 1988), but in a more recent review the limiting factor in
raw starch hydrolysis was attributed to .alpha.-amylase activity
(Gorgens et al., 2015). The type of starchy biomass (used as
substrate) is likely to affect the ratio of amylases, but if a
recombinant amylolytic yeast is able to produce highly active
enzymes, an exact ratio should not be a limiting factor.
During cultivation on 200 gl.sup.-1 raw corn starch, simultaneous
expression of the .alpha.-amylase and glucoamylase combinations in
S. cerevisiae resulted in varying ethanol yields (FIGS. 4a and b).
After 72 hours, the carbon conversion displayed by the S.
cerevisiae Y294[TemG_Opt-TemA_Nat] strain was 2.7-fold higher than
the S. cerevisiae Y294[AmyA-GlaA] benchmark strain. The S.
cerevisiae Y294[TemG_Opt-ApuA_Nat] and Y294[TemG_Opt-AteA_Nat]
strains also outperformed the S. cerevisiae Y294[AmyA-GlaA]
benchmark strain (FIG. 4a) in the early stages of fermentation
(>2.4-fold higher ethanol concentrations after 48 hours).
Substantially higher ethanol concentrations were obtained, compared
to the modified amylolytic yeast strain constructed by Yamakawa et
al. (2012), which produced 46.5 gl.sup.-1 ethanol from 200
gl.sup.-1 of raw corn starch. Furthermore, these results showed
considerable improvements when compared to amylolytic CBP systems
listed in a recent review by Salehi Jouzani and Taherzadeh, (2015).
The carbon conversion displayed by the S. cerevisiae
Y294[TemG_Opt-TemA_Nat] strain on raw corn starch (Table 3)
represented the highest reported for amylolytic S. cerevisiae Y294
strains in fermentations with high substrate loading and low
inoculums.
Overall, S. cerevisiae recombinant strains with higher levels of
glucoamylase, i.e. those expressing the temG_Opt glucoamylase,
hydrolysed starch better than the S. cerevisiae Y294 strains with
the temG_Nat glucoamylase. However, S. cerevisiae
Y294[TemG_Opt-TemA_Nat] displayed a significantly higher carbon
conversion (.about.1.6-2.0 fold) compared any of the other
recombinant S. cerevisiae Y294 strains expressing the temG_Opt
glucoamylase (Table 3). This suggested that there was a unique
synergistic effect between the T. emersonii TemG_Opt and TemA_Nat
enzymes that outperformed the other TemG_Opt-.alpha.-amylase
combinations.
A synergistic effect was also observed for the A. tubingensis
enzyme combination. At 192 hours, the carbon conversion displayed
by the S. cerevisiae Y294[GlaA-AmyA] strain (54%) was 9% higher
than the carbon conversion displayed by the S. cerevisiae
Y294[TemG_Opt-AmyA] strain (49%) (Table 3), even though TemG_Opt
was superior to GlaA in terms of activity (FIG. 3). This
highlighted the importance of comparing different enzyme
combinations in the chosen expression host. Even though
extracellular amylase activities differed (FIGS. 2 and 3), enzymes
originating from the same host may have a superior synergistic
hydrolytic effect as a result of their modes of action and affinity
for raw starch. Prese ki et al. (2013) developed a mathematical
model to explain the synergism between a glucoamylase and two
.alpha.-amylases (in different combinations) and showed that the
type and combinations of amylases affected enzyme synergy.
Furthermore, whether an .alpha.-amylases is classified as
"liquefying" or "saccharifying" may also attribute to the synergist
relationship (Liakopoulou-Kyriakides et al., 2001).
The AmyA .alpha.-amylase displayed a greater extracellular activity
on soluble starch, compared to the AteA_Nat enzyme (FIG. 2a).
However, during fermentation studies the AteA_Nat .alpha.-amylase
combinations facilitated a faster rate of raw starch conversion
compared to the enzyme combinations with AmyA (FIG. 4). AteA_Nat
also contributed to higher ethanol productivity levels (compared to
AmyA) when combined with the TemG_Opt and TemG_Nat glucoamylases,
respectively (FIG. 4 and Table 3). This suggested that AteA_Nat may
have performed better on raw starch compared to the AmyA enzyme, or
it had a superior synergistic effect with the TemG
glucoamylase.
Dissimilarly, the extracellular activity produced by the S.
cerevisiae Y294[ApuA_Nat] strain (expressing the native
.alpha.-amylase from A. pullulans) was 2.7-fold higher than that of
the S. cerevisiae Y294[AmyA] benchmark strain (FIGS. 2a and b), but
overall the carbon conversion displayed by the amylolytic S.
cerevisiae Y294[TemG_Opt-ApuA_Nat] strain was 13% lower than the S.
cerevisiae Y294[TemG_Opt-AmyA] strain (Table 3). Therefore, AmyA
may either have had improved raw starch converting ability, or a
better synergistic relationship with TemG_Opt, compared to ApuA_Nat
(FIG. 4a). Chi et al. (2009) demonstrated that the glucoamylase
from A. pullulans hydrolysed potato starch granules (type-B
crystallinity) better than raw corn starch granules (type-A
crystallinity), although type-B starch structures are usually more
resistant to enzyme hydrolysis (Man et al., 2013). Corn starch has
a higher amylose content and smaller granule diameter compared to
potato starch (Hii et al., 2012) and the combination of these
properties are known to influence the rate and extent of starch
hydrolysis (Naguleswaran et al., 2013). Results from this study
(FIGS. 2 and 4) highlighted a prime example where starch structure
affected the action of different amylolytic enzymes.
Although S. cerevisiae is known for its ethanol tolerance, the Y294
strains were inhibited by fermentation conditions at an incubation
temperature of 30.degree. C. and thus ethanol concentrations did
not exceed 63 gl.sup.-1 (FIGS. 5 and 6). The poor fermentative
performance by the S. cerevisiae Y294 laboratory strain was not as
a result of inadequate recombinant protein secretion or low
enzymatic activity, since glucose concentrations increased rapidly
throughout the fermentation with the S. cerevisiae
Y294[TemG_Opt-TemA_Nat] strain (FIG. 4b).
Raw starch fermentation by recombinant S. cerevisiae strains is
often disadvantaged by long cultivations times required for
sufficient enzyme secretion. However, it was clear from the
fermentation results for the S. cerevisiae Y294[TemG_Opt-TemA_Nat]
strain (FIG. 5) that volumetric productivity and starch conversion
rates were high. Furthermore, a cultivation temperature of
26.degree. C. relieved physiological stress on the yeast cells,
allowing for improved glucose conversion. After 192 hours, the
carbon conversion displayed by the S. cerevisiae
Y294[TemG_Opt-TemA_Nat] strain was the similar (81-85%) for the 100
ml serum bottles and bioreactor fermentations, respectively (Table
4.3 and FIG. 4.5b). Thus suggesting that the lower temperature was
the main factor to favour glucose fermentation and that the
extracellular enzyme activity was not significantly affected by a
lower temperature (since the final carbon conversion remained the
same at both fermentation temperatures). Therefore, decreasing the
fermentation temperature confirmed that it was possible to increase
the conversion of glucose to ethanol and improve the theoretical
ethanol yield.
Schmidt et al. (2006) provided several definitions for ethanol
tolerance, one of which was the effect of ethanol concentrations on
the ability of a cell to metabolise sugar. Biochemical and
physiological responses occur when yeast are exposed to
accumulating ethanol concentrations (Schmidt et al., 2006) and as a
result S. cerevisiae Y294 strains were likely to experience
compromised membrane structure and protein function. The presence
of ethanol changes the composition of the phospholipid bilayer
making it permeable to small molecules. Since many cellular
functions rely on membrane integrity, high ethanol concentrations
can have a number of adverse effects on the yeast cell. In this
study, the negative effects of ethanol accumulation could be
avoided by lowering the fermentation temperature to 26.degree.
C.
Conclusion
Currently, industry lacks the implementation of an amylolytic CBP
yeast that simultaneously expresses both an .alpha.-amylase and
glucoamylase. This study focused on the selection of highly active
amylases with the ability to convert raw starch to glucose. This
led to the identification and evaluation of novel amylase
combinations for the hydrolysis of raw starch. The recombinant S.
cerevisiae Y294[TemG_Opt-TemA_Nat] strain was superior in its
ability to convert 85% of the available carbon in 200 gl.sup.-1 raw
corn starch fermentation within 192 hours. Thus, this unique
TemG_Opt-TemA_Nat enzyme combination represents a promising
candidate for the industrial conversion of uncooked starch.
Example 2: Construction of Amylolytic CBP S. cerevisiae Ethanol
Red.TM. and M2n Strains
Materials and Methods
Media and Cultivation Conditions
All chemicals were of analytical grade and were obtained from Merck
(Darmstadt, Germany), unless otherwise stated. Escherichia coli
DH5.alpha. (Takara Bio Inc.) was used for vector propagation. The
E. coli transformants were selected for on Luria Bertani agar
(Sigma-Aldrich, Germany), containing 100 .mu.gml.sup.-1 ampicillin
and cultivated at 37.degree. C. in Terrific Broth (12 gl.sup.-1
tryptone, 24 gl.sup.-1 yeast extract, 4 mll.sup.-1 glycerol, 0.1 M
potassium phosphate buffer) containing 100 .mu.gml.sup.-1
ampicillin for selective pressure (Sambrook et al., 1989).
The S. cerevisiae parental strains were maintained on YPD agar
plates (10 gl.sup.-1 yeast extract, 20 gl.sup.-1 peptone, 20
gl.sup.-1 glucose and 20 gl.sup.-1 agar). The S. cerevisiae Y294
transformants were selected for and maintained on SC.sup.-URA agar
plates (6.7 gl.sup.-1 yeast nitrogen base without amino acids
(BD-Diagnostic Systems, Sparks, Md.), 20 gl.sup.-1 glucose and 1.5
gl.sup.-1 yeast synthetic drop-out medium supplements
(Sigma-Aldrich, Germany) and 20 gl.sup.-1 agar). S. cerevisiae
strains were aerobically cultivated on a rotary shaker (200 rpm) at
30.degree. C., in 125 ml Erlenmeyer flasks containing 20 ml double
strength SC.sup.-URA medium (2.times.SC.sup.-URA containing 13.4
gl.sup.-1 yeast nitrogen base without amino acids (BD-Diagnostic
Systems, Sparks, Md.), 20 gl.sup.-1 glucose and 3 gl.sup.-1 yeast
synthetic drop-out medium supplements). Fermentation media for S.
cerevisiae Y294 strains comprised of 2.times.SC.sup.-URA containing
5 gl.sup.-1 glucose and 200 gl.sup.-1 raw corn starch, whereas the
medium for S. cerevisiae Ethanol Red.TM. from Fermentis and M2n
strains was YP containing 5 gl.sup.-1 glucose and 200 gl.sup.-1 raw
corn starch. Ampicillin (100 .mu.gml.sup.-1) and streptomycin (50
.mu.gml.sup.-1) were added to inhibit bacterial contamination. All
cultures were inoculated to a concentration of 1.times.10.sup.6
cellsml.sup.-1, unless otherwise stated.
SC media (yeast synthetic drop-out medium omitted) containing 2%
starch was used to maintain industrial transformants. The S.
cerevisiae Ethanol Red.TM. and M2n transformants were selected for
on SC-Ac plates (SC plates with (NH.sub.4).sub.2SO.sub.4 replaced
by 0.6 gl.sup.-1 acetamide and 6.6 gl.sup.-1 K.sub.2SO.sub.4) and
transferred to SC-Acr plates (SC-Ac with 0.71 gl.sup.-1 acrylamide
replacing the acetamide). For plate assays, 2% soluble starch was
added to SC-Ac and SC-Acr plates. SC-Fac plates (SC media
containing 2.3 gl.sup.-1 fluoroacetamide) was used to remove the
yBBH1-amdSYM vector from the transformants. The pH in all the media
was adjusted to 6.0 with NAOH.
Strains and Plasmids
The genotypes of the bacterial and yeast strains, as well as the
plasmids used in this study, are summarised in Table 4.
TABLE-US-00004 TABLE 4 Strains and plasmids used in this study
Reference/ Strains and plasmids Genotype Source E. coli DH5.alpha.
supE44 .DELTA.lacU169 (.PHI.80lacZ.DELTA.M15) hsdR17 recA1 Sambrook
et al. endA1 gyrA96 thi-1 relA1 (1989) S. cerevisiae strains Y294
.alpha. leu2-3,112 ura3-52 his3 trp1-289 ATCC 201160 Y294[amdSYM]
URA3 TEF.sub.P-amdS-TEF.sub.T This study Y294[TemG_Opt- URA3
ENO1.sub.P-temG_Opt-ENO1.sub.T; This study TemA_Nat]
ENO1.sub.P-temA_Opt-ENO1.sub.T Ethanol Red .TM..sup.1 MATa/.alpha.
prototroph Fermentis, Lesaffre, France M2n MATa/.alpha. prototroph
Favaro et al. (2015) Ethanol Red .TM. T1.sup.2 .delta.-integration
of ENO1.sub.p-temG_Opt-ENO1.sub.T; This study
ENO1.sub.P-temA_Nat-ENO1.sub.T Ethanol Red .TM. T12.sup.2
.delta.-integration of ENO1.sub.P-temG_Opt-ENO1.sub.T; This study
ENO1.sub.P-temA_Nat-ENO1.sub.T Ethanol Red .TM.TemA_Nat
.delta.-integration of ENO1.sub.P-temA_Nat-ENO1.sub.T This study
M2n T1.sup.2 .delta.-integration of ENO1.sub.P-temG_Opt-ENO1.sub.T;
This study ENO1.sub.P-temA_Nat-ENO1.sub.T M2n T2.sup.2
.delta.-integration of ENO1.sub.P-temG_Opt-ENO1.sub.T; This study
ENO1.sub.P-temA_Nat-ENO1.sub.T M2n[TLG1-SFA1] TLG1 and SFA1
multiple copy integration Favaro et al. (2015) Plasmids yBBH1 bla
URA3 ENO1.sub.P-ENO1.sub.T Njokweni et al. (2012)
yBBH1-TemA_Nat.sup.3 bla URA3 ENO1.sub.P-temA_Nat-ENO1.sub.T This
study yBBH1-TemG_Opt.sup.4 bla URA3 ENO1.sub.P-temG_Opt-ENO1.sub.T
This study yBBH1-TemG_Opt- bla URA3 ENO1.sub.P-temG_Opt-ENO1.sub.T;
This study TemA_Nat ENO1.sub.P-temA_Nat-ENO1.sub.T pUG-amdSYM.sup.5
bla TEF.sub.P-amdS-TEF.sub.T Solis-Escalante et al. (2013)
yBBH1-amdSYM bla URA3 TEF.sub.P-amdS-TEF.sub.T This study
.sup.1Ethanol Red .TM. Version 1, referred to as Ethanol Red .TM.
.sup.2Amylolytic transformants (T) contain integrated copies of
ENO1.sub.P-temA_Nat-ENO1.sub.T and ENO1.sub.P-temG_Opt-ENO1.sub.T
gene cassettes, the number indicates the transformant number during
the screening process .sup.3Accession no. XM_013469492 for the
native T. emersonii .alpha.-amylase (temG_Nat) .sup.4Accession no.
AJ304803 for the native T. emersonii glucoamylase (temG_Opt encodes
for the codon-optimized gene) .sup.5Assession no. P30669 for
pUG-amdSYM plasmid
DNA Manipulations
Standard protocols were followed for all DNA manipulations and E.
coli transformations (Sambrook et al., 1989). The enzymes used for
restriction digests and ligations were purchased from Inqaba Biotec
and used as recommended by the supplier. Digested DNA was eluted
from 0.8% agarose gels using the Zymoclean.TM. Gel DNA Recovery Kit
(Zymo Research, USA). The temA_Nat and temG_Opt gene cassettes
(ENO1 promoter and terminator) (FIG. 1b) were amplified through PCR
using Delta-ENO1 primers (Table 5), together with the
yBBH1[TemA_Nat] and yBBH1[TemG_Opt] vectors (see Example 1),
respectively, as template.
Plasmid Construction
The TEF.sub.P-amdSYM-TEF.sub.T gene cassette was amplified from
pUG-amdSYM through PCR using amdSYMCas primers (Table 5) and cloned
onto yBBH1 using yeast-mediated ligation (YML) yielding plasmid
yBBH1-amdSYM (FIG. 6a). The Ashbya gossypii TEF promoter regulated
the expression of the acetamidase-encoding gene (amdS) for the
selection of transformants on SC-Ac plates. The yBBH1-amdSYM
plasmid was retrieved from the S. cerevisiae Y294[amdSym] strain
and transformed into E. coli DH5.alpha. in order to obtain a high
concentration of plasmid DNA. Plasmid DNA was isolated using the
High Pure Plasmid Isolation kit (Roche, Germany) and sequence
verification was performed by the dideoxy chain termination method,
with an ABI PRISM.TM. 3100 Genetic Analyser (CAF, Stellenbosch
University).
TABLE-US-00005 TABLE 5 PCR primers designed and used in this study
with the relevant restriction sites underlined (EcoRI = gaattc;
XhoI = ctcgag, BamHI = ggatcc, BglII = agatct) SEQ Primer name
Sequence (5'-3') ID NO: amdSYMCas: L
ccgcgcgttggccgattcattaatccaggatccacatggaggcccagaataccctccttga- c 37
amdSYMCas: R
gggcctcttcgctattacgccagagcttagatctcagtatagcgaccagcattcacatact- taa
38 Delta-
tggaataaaaatccactatcgtctatcaactaatagttatattatcaatatattatcatatacg
39- ENO1p: L
gtgttaagatgatgacataagttatgagaagctgtcggatcccaattaatgtgagttacctcac -
Delta-
tgagatatatgtgggtaattagataattgttgggattccattgttgataaaggctataatatta
40- ENO1t: R
ggtatacagaatatactagaagttctcctcgaggatagatctcctatgcggtgtgaaataccgc -
TemG_Opt: L
ttatcaacacacaaacactaaatcaaagaattcatggcctccttagtcgcaggtgcctta 4- 1
TemG_Opt: R
gactagaaggcttaatcaaaagctctcgagtcattgccaagagtcgtccaagattgcggt 4- 2
TemA_Nat: L
tgcttatcaacacacaaacactaaatcaaagaattcatgacgcctttcgtcctcacggcc 4- 3
TemA_Nat: R
ggactagaaggcttaatcaaaagctctcgagctatctccatgtgtcgacaatcgtctccg 4-
4
Yeast Transformations
Electro-competent S. cerevisiae Y294, Ethanol Red.TM. and M2n cells
were prepared according to Cho et al. (1999) and transformed by
means of electroporation using a BioRad system
(GenePluserXcell.TM., Bio-Rad, Hercules, Calif.). For the
transformation of industrial strains, amylases (temA_Nat and
temG_Opt ENO1 linear DNA cassettes) and the yBBH1-amdSYM vector
containing the selection marker (FIG. 6) were simultaneously
transformed into the genomes of the yeasts. After electroporation,
1 ml of YPDS was immediately added to the cuvettes. Cells were
incubated at 30.degree. C. for 3 hours. Transformants were selected
for by plating the transformation mix on to SC-Ac plates containing
2% starch (adapted from Solis-Escalante et al., 2013) and incubated
at 30.degree. C. for 4 days. The integration of the linear
expression cassette DNA into the yeast genome was confirmed by PCR
using gene specific primers (Table 5).
Marker Recycling
Plasmid curing was performed on the industrial recombinant strains
as described by Solis-Escalante et al. (2013). The removal of the
yBBH1-amdSYM containing the acetamide marker was achieved by
growing cells overnight in 5 ml liquid YPD and transferring 20
.mu.l to a 125 ml Erlenmeyer flask containing 10 mL SC-Fac.
Marker-free single colonies were obtained by plating 100 .mu.l of
culture on SC-Fac solid media containing 2% starch and confirmed by
colony PCR. The genomic DNA of the amylolytic strains was isolated
using the ZR fungal/bacterial DNA miniprep kit (Zymo Research, USA)
and it was then used as a template for real-time PCR.
Quantitative PCR
Oligo primers for real-time PCR were designed using IDT's
PrimerQuest Tool (eu.idtdna.com/PrimerQuest/Home/Index). Special
attention was given to primer length (18-22 bp), annealing
temperature (58-62.degree. C.), base composition, 3'-end stability
and amplicon size (75-100 bp). All primers were synthesised by
Inqaba Biotech (South Africa) with reverse phase cartridge
purification and are listed in Table 6. The performance of all
primers was experimentally confirmed by conventional PCR to ensure
that there was no formation of primer dimers and confirm the
amplification of a single region with the correct amplicon
length.
TABLE-US-00006 TABLE 6 List of candidate reference genes and target
genes including details of primers and amplicons for each gene
Amplicon SEQ length ID Gene name (bp) Primers (5'-3') NO: URA3 92
L: cgtggatgatgtggtctctac 45 R: gttcaccctctaccttagcatc 46 temA_Nat
100 L: gcgatgtcactgagaggatcta 47 R: gaaatccagatggccgtgaa 48
temG_Opt 95 L: tacaggtggtttgggtgaac 49 R: ctctcaatgctggaccatctc
50
Real-time PCR was carried out on a StepOne real time Polymerase
Chain Reaction (PCR) instrument (Applied Biosystems) using
white-walled PCR plates (96 wells). A .times.2 KAPA HRM Fast Master
Mix (containing a fast proof-reading polymerase, dNTPs, stabilisers
and EvaGreen.RTM. dye) was used according to the manufacturer's
instructions (KAPA Biosystems). Reactions were prepared in a total
volume of 20 .mu.l containing, 2.5 mM MgCl.sub.2, 0.2 .mu.M of each
primer and 1-10 ng DNA. The cycle conditions were set as follows:
initial template denaturation at 95.degree. C. for 30 seconds,
followed by 45 cycles of denaturation at 95.degree. C. for 5
seconds and combined primer annealing/elongation at 60.degree. C.
for 20 seconds and a final denaturation at 95.degree. C. for 1
minute to ensure all amplicons were fully melted. The
yBBH1-TemG_Opt-TemA_Nat plasmid DNA was used to set up the standard
curves (starting with 1.times.10.sup.7 copies and making a 1:10
serial dilution) using primer pairs listed in Table 6. Genomic DNA
concentrations were standardised to 10 ng for all samples. The PCR
efficiency for each of the primer sets was calculated using StepOne
software (Applied Biosystems). The number of copies of the temG_Opt
and temA_Nat genes was calculated using the standard curve method
using the URA3 gene as reference gene.
Raw Starch Fermentations
The S. cerevisiae Y294 precultures were cultured in 100 ml
2.times.SC.sup.-URA medium in 500 ml Erlenmeyer flasks, and the S.
cerevisiae Ethanol Red.TM. and M2n precultures were cultivated
similarly in YPD medium. All precultures were incubated at
30.degree. C. with agitation at 200 rpms until stationary phase. S.
cerevisiae Y294 fermentations were performed in 2.times.SC.sup.-URA
media, whereas S. cerevisiae Ethanol Red.TM. and M2n fermentations
were performed in YP media (10 gl.sup.-1 yeast extract and 20
gl.sup.-1 l peptone). All media was supplemented with 200 gl.sup.-1
raw corn starch and 5 gl.sup.-1 glucose as carbohydrate sources and
inoculated with a 10% (vv.sup.-1) inoculum from the stationary
preculture. Ampicillin (100 .mu.gml.sup.-1) and streptomycin (50
.mu.gml.sup.-1) were added to inhibit bacterial contamination.
Agitation and incubation were performed on a magnetic multi-stirrer
platform (Velp Scientifica, Italy) at 30.degree. C. and 37.degree.
C., with daily sampling through a syringe needle pierced through
the rubber stopper.
Exogenous enzymes used in the fermentation processes were
STARGEN.TM. 002 GSHE (now referred to as STARGEN.TM.), obtained
from Dupont Industrial Biosciences (Palo Alto, Calif.), with an
activity minimum of 570 GAUgm.sup.-1 (www.genencor.com) and used
according to the manufacturer's instructions. STARGEN.TM. contained
Aspergillus kawachii .alpha.-amylase expressed in Trichoderma
reesei and a glucoamylase from T. reesei that works synergistically
to hydrolyse granular starch to glucose (Huang et al., 2015).
Exogenous amyloglucosidase (E.C. 3.2.1.3) from Aspergillus niger
was purchased from Sigma-Aldrich and used to spike the
fermentations with extra glucoamylase enzyme (now referred to as
commercial glucoamylase).
For bioreactor experiments with the Ethanol Red.TM. T12 strain,
precultures were cultivated in 400 ml YPD in 2 liter Erlenmeyer
flasks at 30.degree. C. Fermentations were performed in a Minifors
2 bioreactor (INFORS HT, Bottmingen, Switzerland) containing YP
supplemented with 200 gl.sup.-1 raw corn starch and 5 gl.sup.-1
glucose as carbohydrate source. A 10% (vv.sup.-1) inoculum was used
in a total working volume of 3 liters. Ampicillin (100
.mu.gml.sup.-1) and streptomycin (50 .mu.gml.sup.-1) were added to
inhibit bacterial contamination. Fermentations were carried out at
30.degree. C., 34.degree. C. and 37.degree. C., with agitation at
300 rpm.
HPLC and Analytical Methods
Ethanol, glucose, maltose, glycerol and acetic acid concentrations
were quantified with high performance liquid chromatography (HPLC)
using a Surveyor Plus liquid chromatograph (Thermo Scientific)
consisting of a liquid chromatography pump, autosampler and
refractive index (RI) detector. The compounds were separated on a
Rezex RHM Monosaccharide 7.8.times.300 mm column (00H0132-K0,
Phenomenex) at 80.degree. C. with 5 mM H.sub.2SO.sub.4 as mobile
phase at a flow rate of 0.6 mlmin.sup.-1.
The theoretical CO.sub.2 concentrations were calculated according
to Favaro et al. (2015). The available carbon (mol C in 100%
hydrolysed substrate) was calculated based on the available glucose
equivalents and the carbon conversion is defined as the percentage
starch converted to fermentable products on a mol carbon basis.
This carbon conversion was calculated from ethanol, glucose,
maltose, glycerol, acetic acid and CO.sub.2 concentrations. The
ethanol yield (% of the theoretical yield) was calculated as the
amount of ethanol produced per gram of consumed sugar. The ethanol
rate of productivity was calculated based on ethanol titres
produced per hour (gl.sup.-1h.sup.-1).
Statistical Analysis
Data was analysed using the Student's t-test.
Results
The T. emersonii temA_Nat and temG_Opt genes encode for valuable
amylase enzymes for use in the production of biofuel and are
produced and secreted during cultivation on raw corn starch. The
linear ENO1.sub.P-temA_Nat-ENO1.sub.T and
ENO1.sub.P-temG_Opt-ENO1.sub.T DNA gene cassettes (FIG. 6b),
flanked by the .delta. sequence, were amplified and integrated into
the .delta.-integration sites in the S. cerevisiae Ethanol Red.TM.
and M2n industrial strains' genomes, in order to generate
multi-copy integrants (Kim et al., 2011). The amdS gene was present
on an episomal vector (FIG. 6a) to enable plasmid curing for easy
recycling of the marker.
Industrial Strain Screening
S. cerevisiae transformants were screened on SC plates containing
2% corn starch and those producing zones of hydrolysis were
selected for further testing. PCR was used to confirm the
integration of both ENO1.sub.P-temA_Nat-ENO1.sub.T and
ENO1.sub.P-temG_Opt-ENO1.sub.T gene cassettes. The four strains
showing the highest extracellular amylase activity were then
evaluated under fermentative conditions (FIGS. 7a and 7b).
Significant differences in the carbon conversion displayed by the
industrial strains was noted during the early stages of
fermentation (FIG. 7b). However, after 192 hours the carbon
conversion started to plateau, representing an approximate 80%
conversion of corn starch. The S. cerevisiae Ethanol Red.TM. T12
and M2n T1 strains hydrolysed starch and fermented the sugars
quicker than the S. cerevisiae Ethanol Red.TM. T1 and M2n T2
strains (FIG. 7b and Table 7). They were therefore selected for
further evaluation under different fermentation conditions.
Plasmid curing of the strains was performed by plating cultures
onto SC-FAc plates containing 2% soluble corn starch. Quantitative
PCR assays were performed using the genomic DNA from the cured
amylolytic S. cerevisiae transformants, in order to determine the
number of integrated copies of both temA_Nat and temG_Opt genes,
respectively (FIG. 7d). The S. cerevisiae Ethanol Red.TM. T1, M2n
T1 and M2n T2 strains contained single copies of temA_Nat and
temG_Opt gene cassettes, whereas the S. cerevisiae Ethanol Red.TM.
T12 contained 1 copy of temA_Nat and 2 copies of temG_Opt.
TABLE-US-00007 TABLE 7 Product formation by S. cerevisiae strains
after 144 hours of fermentation at 30.degree. C. Ethanol Ethanol
M2n M2n S. cerevisiae Red .TM. T1 Red .TM. T12 T1 T2 Substrate (g
l.sup.-1) Raw starch weighed 200 200 200 200 Glucose weighed 5 5 5
5 Raw starch (dry weight) 185 185 185 185 Glucose equivalent 208.5
208.5 208.5 208.5 Products (g l.sup.-1) Glucose 0.82 0.67 0.60 0.72
Glycerol 2.39 3.40 1.92 2.29 Acetic acid 0.49 0.46 0.76 0.35
Ethanol 57.76 74.19 72.19 64.68 Maltose 0.99 1.09 1.01 1.08
CO.sub.2.sup.1 55.25 70.94 69.05 61.87 Total 117.68 150.76 145.53
131.00 Carbon conversion (%) 56.44 72.31 69.80 62.83 Ethanol
yield.sup.2 (% of 55.41 71.17 69.25 62.05 theoretical yield)
Ethanol rate of 0.40 0.52 0.50 0.45 productivity.sup.3
.sup.1CO.sub.2 concentrations were deduced from the ethanol
produced .sup.2Ethanol yield (% of the theoretical yield) was
calculated as the amount of ethanol produced per gram of consumed
glucose .sup.3Ethanol rate of productivity was calculated based
ethanol titres produced per hour (g l.sup.-1 h.sup.-1)
The fermentation vigour of the amylolytic S. cerevisiae Ethanol
Red.TM. T12 strain at 30.degree. C. and 37.degree. C. was compared
to the laboratory S. cerevisiae Y294[TemG_Opt-TemA_Nat] strain at
30.degree. C. (FIG. 8). The S. cerevisiae Ethanol Red.TM. T12
strain was able to ferment all the available glucose (FIG. 8b) at a
fermentation temperature of 30.degree. C. and produced
significantly less glycerol during the fermentation (FIG. 8d). This
indicated a more efficient carbon conversion for ethanol (Bideaux
et al., 2006). However, at a temperature of 37.degree. C., ethanol
levels did not increase significantly after 144 hours (FIG. 8a) and
high level of residual glucose were present (>40 gl.sup.-1 after
264 hours). Maltose concentrations were similar at both
fermentation temperatures (FIG. 8c).
The evaluation of different media conditions (FIG. 9) was
subsequently undertaken in order to determine whether buffered
fermentation media (pH 5), the type of media (YP versus SC) or the
addition of extra nitrogen (in the form of
(NH.sub.4).sub.2SO.sub.4) could increase the efficiency of glucose
fermentation by the S. cerevisiae Ethanol Red.TM. T12 strain at a
fermentation temperature of 37.degree. C. YP starch media
(unbuffered) had a pH lower than 5 and this was more favourable for
ethanol production, compared to the buffered YP broth (pH 5) (FIG.
9a). The addition of extra ammonium sulphate (10 gl.sup.-1) to the
SC buffered fermentation broth did not increase ethanol
concentrations or carbon conversion (FIGS. 9a and 9d), indicating
sufficient nitrogen levels in the fermentation broth.
Increased residual glucose concentrations were observed when YP
media was used (FIG. 9b), while higher glycerol concentrations were
noted when the fermentation was performed in SC media (FIG. 9c). YP
is more nutrient rich compared to the SC medium and a decreased
formation of NADH formed from biosynthesis, therefore less
glycerol. The higher glycerol concentrations contributed to
increased carbon conversion values, especially during the first 120
hours of fermentation. Overall, the results in FIG. 9 showed that
the media composition (SC vs YP and the pH) affected the ethanol
and glycerol production. However, changes in the type of media only
affected the percentage carbon conversion during the first 120
hours of fermentation. After 192 hours, the differences in carbon
conversion values s was less apparent (between 92-100%).
Fermentations with STARGEN.TM.
The recommended STARGEN.TM. dosage was calculated as 1.42
.mu.lg.sup.-1 starch, according to the manufacturer's
specifications. The amylolytic S. cerevisiae Ethanol Red.TM. T12
and M2n T1 strains were compared to a simulated conventional SSF
process (parental S. cerevisiae Ethanol Red.TM./M2n
strains+STARGEN.TM.) at 200 gl.sup.-1 corn starch. Three different
enzyme dosages were evaluated based on the percentage of the
recommended enzyme loading: 2.8 .mu.l (10%), 5.6 .mu.l (20%) and 14
.mu.l (50%) and compared to the SSF, which had 28 .mu.l STARGEN.TM.
per 100 ml (representing 100% of the recommended dosage). The
addition of exogenous enzymes significantly increased ethanol
concentrations and enhanced ethanol productivity (ethanol
gl.sup.-1h.sup.-1) during the first 72 hours of fermentation (FIGS.
10 and 11).
At a fermentation temperature of 30.degree. C. the ethanol profiles
for the S. cerevisiae Ethanol Red.TM. and M2n parental strains were
similar for the respective condition (FIGS. 10a and 11a). By 48
hours, the S. cerevisiae Ethanol Red.TM. T1 strain supplemented
with 2.8 ul STARGEN.TM. produced the same amount of ethanol (52
gl.sup.-1) and displayed a similar carbon conversion (50%) to that
of the control SSF process with untransformed S. cerevisiae Ethanol
Red.TM. supplemented with 28 .mu.l STARGEN.TM. (Table 8). A similar
trend was observed for the S. cerevisiae M2n T1 strain supplemented
with 2.8 .mu.l STARGEN.TM. compared to the S. cerevisiae M2n
parental strain (FIGS. 11a and c).
After 96 hours, ethanol produced by the S. cerevisiae Ethanol Red
T12 strain supplemented with 2.8 .mu.l STARGEN (90.4 gl.sup.-1) was
similar to the amount of ethanol produced by the S. cerevisiae
Ethanol Red T12 strain supplemented with 5.6 .mu.l STARGEN (92.0
gl.sup.-1) (FIG. 10). The carbon conversion displayed by these two
strains was also similar (between 88-90%), at 96 hours (FIG. 10).
This represented a significant increase in ethanol compared to the
S. cerevisiae Ethanol Red control strain supplement with 28 .mu.l
STARGEN, which produced 76.8 gl.sup.-1 ethanol and displayed a 75%
carbon conversion after 96 hours. Therefore, the addition of 2.8
.mu.l STARGEN (10% of the recommended dosage) was sufficient to
produce results that were comparable to an SSF control.
Similar results and trends were observed for the S. cerevisiae M2n
strains at a fermentation temperature of 30.degree. C., compared to
the S. cerevisiae Ethanol Red.TM. equivalent strains (FIGS. 10 and
11). However, the final ethanol concentration for the S. cerevisiae
M2n T1 transformant was higher >10 gl.sup.-1 after 192 hours
(p=0.0392). At 30.degree. C., the low residual levels of glucose
and maltose in the fermentation broth (Table 8) indicated a rapid
sugar uptake by all the amylolytic strains.
TABLE-US-00008 TABLE 8 Product formation by S. cerevisiae Ethanol
Red .TM. and M2n strains after 192 hours of fermentation at
30.degree. C. in YP media, supplemented with different STARGEN .TM.
dosages Ethanol Ethanol Ethanol Red .TM. M2n Red .TM. S. cerevisiae
strains Red .TM. M2n T12 T1 T12 STARGEN .TM. added 28 28 2.8 2.8
5.6 (.mu.l) Substrate (g l.sup.-1) Raw starch weighed 200 200 200
200 200 Glucose weighed 5 5 5 5 5 Raw starch (dry 185 185 185 185
185 weight) Glucose equivalent 208.5 208.5 208.5 208.5 208.5
Products (g l.sup.-1) Glucose 0.02 0.31 0.02 3.28 0.12 Glycerol
4.07 4.30 4.76 4.59 5.22 Acetic acid 0.00 0 0.90 0.31 0.96 Ethanol
97.23 98.49 98.37 99.08 100.32 Maltose 0.79 0.71 0.31 0.37 0.26
CO.sub.2.sup.1 93.00 94.21 94.09 94.77 95.96 Total 195.11 198.02
198.44 202.40 202.85 Carbon conversion (%) 93.58 94.98 95.17 97.07
97.29 Ethanol yield (% of 93.26 94.48 94.36 95.04 96.23 theoretical
yield).sup.2 Ethanol rate of 0.51 0.51 0.51 0.52 0.52
productivity.sup.3 .sup.1CO.sub.2 concentrations were deduced from
the ethanol produced .sup.2Ethanol yield (% of the theoretical
yield) was calculated as the amount of ethanol produced per gram of
consumed glucose .sup.3Ethanol rate of productivity was calculated
based ethanol titres produced per hour (g l.sup.-1 h.sup.-1)
At 37.degree. C., the S. cerevisiae Ethanol Red T12 strain had a
higher ethanol tolerance and was able to ferment for longer
(compared to the S. cerevisiae M2n T1 strain) producing a 2.3-fold
increase in ethanol concentration at 192 hours (FIGS. 10 and 11).
Although the recombinant S. cerevisiae M2n T1 strain produced more
ethanol at 30.degree. C., it was severely affected at a higher
fermentation temperature (FIG. 11). At 37.degree. C., the ethanol
concentrations plateaued after 48 hours for all the S. cerevisiae
M2n fermentations (FIG. 11 b). The extent of carbon conversion
displayed by the S. cerevisiae Ethanol Red T12 strain was similar
(.about.83%) at the two fermentation temperatures (FIGS. 10c and
d), while the carbon conversion displayed by the S. cerevisiae M2n
T1 strain was 13% higher at 30.degree. C., compared to the carbon
conversion at 37.degree. C. (FIGS. 11c and 11d). Both the
amylolytic S. cerevisiae Ethanol Red T12 and M2n T1 strains had
lower ethanol productivity at 37.degree. C., compared to at
30.degree. C. and residual glucose levels were >40 gl.sup.-1 at
37.degree. C. (data not shown), which represented a large amount of
unfermented glucose. Overall, results showed that temperature
tolerance played a major role on the fermentation vigour of
industrial S. cerevisiae Ethanol Red T12 and M2n T1 strains. The
addition of STARGEN in combination with the amylolytic yeast
strains reduced the fermentation time and increased the carbon
conversion, compared to the control with untransformed strains and
the recommended enzyme dosage.
Strain Comparison
The S. cerevisiae Ethanol Red.TM. T12 and M2n T1 strains were
compared in a small scale fermentation to a previously constructed
amylolytic industrial strain M2n[TLG1-SFA1] (Favaro et al., 2015).
Both the Ethanol Red.TM. T12 and M2n T1 strains performed better
(FIG. 12), producing 50 gl.sup.-1 more ethanol after 240 hours of
fermentation, compared to the M2n[TLG1-SFA1] strain, thus
demonstrating the superior TemG_Opt and TemA_Nat enzyme combination
for raw starch hydrolysis.
Fermentations in 5-Liter Bioreactor
Overall, small scale fermentations demonstrated that the S.
cerevisiae Ethanol Red.TM. T12 strain performed the best at higher
fermentation temperatures. This strain also showed the highest
activity levels during glucose assays because it had more
integrated copies of the temG_Opt gene. Therefore, Ethanol Red.TM.
T12 was evaluated further in bioreactor studies. The main advantage
of the 5-liter bioreactor was a controlled internal temperature.
Results depicted in FIG. 13 showed the effect on ethanol
concentrations and carbon conversion when the fermentation
temperature increased. The internal broth temperature can't be
controlled during serum bottle fermentations and as a result the
internal temperature exceeds that of the incubator's set
temperature by .about.2.degree. C. After 144 hours, .about.67
gl.sup.-1 ethanol was produced by the Ethanol Red.TM. T12 strain
both in the bioreactor with an internal temperature of 37.degree.
C. and in the parallel fermentation in 100 ml serum bottles at
30.degree. C. The strain's fermentative ability is affected (FIG.
13a) and ethanol concentrations do not compare (serum bottles
versus bioreactor) because the temperature of the fermentation
broth affects the rate of starch hydrolysis and subsequently the
glucose available for fermentation to ethanol.
During the 5-liter bioreactor experiments at 37.degree. C., the
Ethanol Red.TM. T12 strain could hydrolyse starch quicker (compared
to bioreactor fermentations at 30.degree. C. and 34.degree. C.) and
the Ethanol Red.TM. T12 strain fermented all the available glucose
to ethanol. After 168 hours, 81 gl.sup.-1 ethanol was produced at
37.degree. C., compared to 64 gl.sup.-1 and 35 gl.sup.-1 ethanol at
34.degree. C. and 30.degree. C., respectively (FIG. 13a).
Furthermore, there was at least a 2-fold increase in ethanol
concentrations at a fermentation temperature of 37.degree. C.
compared to at 30.degree. C. (during the first 7 days of
fermentation). Therefore, these results confirmed that the Ethanol
Red.TM. T12 strain was more robust compared to the S. cerevisiae
Y294 strains (in Example 1) and performed well as a CBP yeast at
37.degree. C.
Ratio Testing
Synergy testing has allowed for an improved use of enzyme
combinations for substrate hydrolysis and fermentation. Enzyme
synergy refers to the action of two or more enzymes acting together
in solution being greater than the sum of their individual actions.
Traditionally, when using the conventional conversion of starch to
ethanol, a higher dosage of glucoamylase has been used. Therefore,
fermentations using the Ethanol Red.TM. T12 strain were performed
with the supplementation of commercial glucoamylase (FIG. 14), in
order to establish how different enzyme dosages affect the rate of
ethanol production.
Fermentations with the Ethanol Red.TM. T12 strain supplemented with
10 .mu.l commercial glucoamylase significantly increased the rate
of ethanol production. After 144 hours, glucoamylase
supplementation resulted in a 29 gl.sup.-1 (44%) increase in the
ethanol concentration. In addition, if the amount of recombinant
enzyme was decreased by a half (5 ml Ethanol Red.TM. T12+5 ml
untransformed Ethanol Red.TM. as inoculum), the ethanol
concentration dropped by 54% at 144 hours (FIG. 14a). FIG. 14b
showed that the trends for carbon conversion were similar to
ethanol concentration trends. This is because the strains were able
to ferment all the available glucose to ethanol at a fermentation
temperature of 30.degree. C.
To further evaluate the optimal enzyme ratio for raw starch
hydrolysis, an Ethanol Red.TM. strain expressing only the temA_Nat
.alpha.-amylase was constructed. FIG. 15 showed the performance of
the Ethanol Red.TM. TemA_Nat strain in combination with different
dosages of commercial glucoamylase during small scale fermentations
at 30.degree. C. Results showed that the Ethanol Red.TM. T12 strain
has a suboptimal ratio and ethanol production could be increased by
either increasing the number of integrated gene copies or by
supplementing the fermentation broth with small dosages of
commercial enzyme. These results further demonstrated that
industrial ethanol production can be improved by the use of a
recombinant amylolytic S. cerevisiae strain.
Discussion
Gene Integration
After the initial screening process, four recombinant strains
expressing the temG_Opt and temA_Nat gene cassettes (the S.
cerevisiae Ethanol Red.TM. T1/T12 and S. cerevisiae M2n T1/T2
strains) were selected for further evaluation (FIG. 7). The S.
cerevisiae M2n T1 strain performed better than the S. cerevisiae
Ethanol Red.TM. T12 strain at 30.degree. C. and achieved a maximum
ethanol titre of 99.4 gl.sup.-1, which was 15% higher than the S.
cerevisiae Ethanol Red.TM. T12 strain, at 192 hours (FIGS. 10a and
11a). However, at fermentations in serum bottles at 37.degree. C.,
it was clear that the S. cerevisiae Ethanol Red.TM. T12
transformant had a greater fermentation vigour and was more ethanol
and temperature tolerant (FIGS. 10b and 11b) compared to the S.
cerevisiae M2n strain.
Results from this study showed significant improvements in starch
hydrolysis and ethanol production when compared to the industrial
S. cerevisiae M2n[TLG1-SFA1] (FIG. 12) and MEL2[TLG1-SFA1]
amylolytic strains (Favaro et al., 2015) that produced 64 gl.sup.-1
ethanol from 200 gl.sup.-1 raw corn starch, corresponding to 55% of
the maximum theoretical ethanol yield, as well as the S. cerevisiae
Mnu.alpha.1[AmyA-GlaA] strain (Viktor et al., 2013) that produced
65.83 gl.sup.-1 ethanol (after 10 days) representing 57% of the
maximum theoretical ethanol yield. Theoretical ethanol yields
obtained from the recombinant industrial strains in this study were
>90% and thus represented a significant improvement on
previously constructed amylolytic strains.
Ethanol concentrations were also higher than those reported for the
amylolytic yeast strain, which produced 46.5 gl.sup.-1 of ethanol
from 200 gl.sup.-1 of raw corn starch after 120 hours of
fermentation (Yamakawa et al., 2012). The amylolytic yeast strains
expressing the temG_Opt and temA_Nat gene cassettes in this study
were superior in their ethanol production, producing >50
gl.sup.-1 and >60 gl.sup.-1 ethanol for the S. cerevisiae
Ethanol Red.TM. T12 and M2n T1 strains, respectively, after 120
hours (FIGS. 10a and 11a). Furthermore, since the amylases were
secreted into the fermentation broth they had increased physical
contact with the starch granules, compared to recombinant yeast
that displayed amylases on the cell's surface (Yamakawa et al.,
2012). This eliminated potential bottlenecks and facilitated
improved starch hydrolysis because the raw starch TemA_Nat and
TemG_Opt amylases were able to penetrate starch granules and create
pores more quickly.
STARGEN.TM. Addition
During fermentation with the amylolytic S. cerevisiae Ethanol
Red.TM. and M2n strains, there was an initial lag phase in carbon
conversion, up until 48 hours (FIGS. 10c and 11c). This was
expected, since the strains first had to adjust to the fermentation
conditions and produce amylases de novo. On the other hand, during
the SSF process with STARGEN.TM. (FIGS. 10a and 11a), the enzymes
were in abundance at the start of the fermentation and rapidly
produced glucose upon addition. Therefore, although S. cerevisiae
Ethanol Red.TM. T12 and M2n T1 strains were able to achieve high
percentages of carbon conversion (FIG. 7b), supplementation with
STARGEN.TM. (FIGS. 10, 11 and 14) increased ethanol productivity at
the start of the fermentation.
In the industrial cold hydrolysis set-up for bioethanol production,
commercial amylase enzymes are only added at the beginning of the
process and therefore their overall efficiency will decrease over
time. However, the amylolytic CBP yeasts of the present invention
were able to continually replenish the recombinant enzymes in the
fermentation broth and thus facilitated increased overall carbon
conversion when the fermentation was supplemented with STARGEN.TM.
(FIGS. 10c,10d, 11c and 11d). The cost of commercial enzyme
addition was estimated at 4.8 US cents per gallon, representing
8.3% of the total possessing costs in ethanol production from corn
(Wong et al., 2010). The recombinant amylolytic S. cerevisiae
Ethanol Red.TM. T12 and M2n T1 strains described herein thus
represent a novel alternative for lowering the enzyme dosage
required for raw starch hydrolysis, as well as being able to
provide continuous amylolytic activity for a continuous cold
fermentations process. Furthermore, the use of amylolytic yeasts of
the present invention would allow for a simplified fermentation
design, since pretreatment steps and costs can be bypassed (Salehi
Jouzani and Taherzadeh, 2015).
Fermentation Temperature
There are a number of other factors that are commonly associated
with a stuck fermentation, including the yeast strain, nitrogen
availability and glucose concentration (Henderson and Block, 2014).
However, fermentation temperature is considered as one of the main
bottlenecks with regards to ethanol production by SSF and CBP
strategies. FIG. 9 showed the performance of the S. cerevisiae
Ethanol Red.TM. T12 strain in different fermentation media and
results confirmed that extra nitrogen (in the form of
(NH.sub.4).sub.2SO.sub.4)) did not increase the fermentation of
glucose to ethanol at a temperature of 37.degree. C. Furthermore,
increasing the pH of the conventional YP fermentation medium (to pH
5) did not improve fermentation conditions. Therefore, a lower pH
was more favourable for starch conversion when using the TemG_Opt
and TemA_Nat enzymes from T. emersonii, which have a pH optimum
around 4-4.5 (Nielsen et al., 2002).
Strain robustness at higher temperatures and ethanol tolerance are
two of the main characteristics that are desired by the biofuel
industry. The demand for higher temperature fermentations began in
the 1980s (Abdel-Banat et al., 2010). High-temperature
fermentations may assist in making the simultaneous fermentation
and ethanol extraction process more suitable for fuel ethanol
production. Operational costs can be decreased (especially in
regions with hot climates where cooling of fermentation vessels is
required) and hydrolysis conditions improved (FIG. 13b). Ethanol
production at high temperatures has several advantages, namely
reduced risk of contamination, increased ethanol recovery, as well
as decreased volumes of cooling waste-water effluent (Banat et al.,
1998).
Currently, the fermentation temperatures used in industry are
between 30-34.degree. C. (Mukhtar et al., 2010). However, the
effect of high temperature is also intensified by ethanol
concentrations that exceed 3% (wv.sup.-1) and this affects the
yeast cell's membrane causing protein denaturation. Therefore,
robust yeasts that can ferment at temperatures above 37.degree. C.
are highly sought after. The internal temperature of a fermentation
vessel typically exceeds incubation/exterior temperatures due to
exogenic metabolic activities, as well as environmental
temperatures in higher-temperature regions. This subsequently
lowers the efficiency of ethanol production. Therefore, it is
important to have a robust yeast that is cable of fermentation when
the temperatures exceed 34.degree. C. (FIG. 13a).
To demonstrate the importance of temperature control and
investigate strain thermostability, fermentations using the Ethanol
Red.TM. T12 strain were performed in parallel, both in serum
bottles (incubated in a walk-in incubator set at 30.degree. C.) and
in a temperature controlled bioreactor (at 30.degree. C.,
34.degree. C. and 37.degree. C.) (FIG. 13). When fermentations at
30.degree. C. were compared (bottles versus bioreactor), a 2-fold
increase in ethanol concentrations was noted between 96 and 168
hours of incubation in serum bottle fermentations (FIG. 13a). This
demonstrated the effect of internal temperature control on ethanol
production from raw corn starch by a CBP yeast. Although there was
unfermented glucose when fermentations were performed at 37.degree.
C. in serum bottles, thus resulting in ethanol levels that
plateaued out around 75-80 gl.sup.-1 (FIG. 10b), the Ethanol
Red.TM. T12 strain could ferment all the glucose at a controlled
temperature of 37.degree. C. (FIG. 13a).
The effect of temperature on fermentation products has been
described by a number of different research groups (Favaro et al.,
2013b; Woo et al. 2014). Although S. cerevisiae is known for its
high ethanol tolerance and relatively high ethanol concentrations,
it still lacks the ability to ferment at higher than normal
temperatures (FIG. 10b). Moreover, ethanol concentrations of
approximately 10% (wv.sup.-1) will reduce the fermentative activity
of yeast by approximately 50% (Henderson and Block, 2014) and
inhibit cell growth and viability. This leads to lower productivity
and lower ethanol yields (Stanley et al., 2010). In order to
improve ethanol tolerance of yeasts, the understanding of the
cellular impact of ethanol toxicity needs to be explored.
Results for the comparison of ethanol production by recombinant S.
cerevisiae Y294 and Ethanol Red.TM. T12 strains were in agreement
with a study by Favaro et al. (2013b). They showed that at
30.degree. C. the laboratory S. cerevisiae Y294 strain had lower
fermentation vigour compared to the industrial strain at 30.degree.
C. The decreased ability to consume glucose could be explained by
the S. cerevisiae Y294 strain displaying an optimum cultivation
temperature around 25.degree. C. and not 30.degree. C. Similarly,
the amylolytic S. cerevisiae Ethanol Red.TM. T12 strain had reduced
fermentation vigour at 37.degree. C. compared to 30.degree. C.
(FIG. 10b), when the internal temperature of the broth was not
controlled.
Glycerol
Reduced glycerol concentrations were observed when lower
fermentation temperatures were used, indicating that better carbon
conversion to ethanol occurred at a fermentation temperature of
30.degree. C. compared to 37.degree. C. (FIG. 8d). Carbon source
utilisation was important for the optimization of ethanol
production (Navarrete et al., 2014) and results showed that the
fermentation media influenced glycerol production (FIG. 8). The
commercially available TransFerm.TM. Yield+ yeast (Mascoma and
Lallemand Biofuels and Distilled Spirits) was engineered to produce
significantly less glycerol during fermentations so that more
carbon can be utilised for ethanol production. In this study, the
accumulating glycerol concentrations were below the conventional
concentration (10 gl.sup.-1) (Huang et al., 2015) and therefore
would not have had a significant effect on the yeast cells.
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SEQUENCE LISTINGS
1
501622PRTRasamsonia emersonii 1Met Thr Pro Phe Val Leu Thr Ala Val
Leu Phe Leu Leu Gly Asn Ala 1 5 10 15 Val Leu Ala Leu Thr Pro Ala
Glu Trp Arg Lys Gln Ser Ile Tyr Phe 20 25 30 Leu Leu Thr Asp Arg
Phe Gly Arg Ala Asp Asn Ser Thr Thr Ala Ala 35 40 45 Cys Asp Val
Thr Glu Arg Ile Tyr Cys Gly Gly Ser Trp Gln Gly Ile 50 55 60 Ile
Asn His Leu Asp Tyr Ile Gln Gly Met Gly Phe Thr Ala Ile Trp 65 70
75 80 Ile Ser Pro Val Thr Glu Gln Leu Pro Gln Asn Thr Gly Glu Gly
Glu 85 90 95 Ala Tyr His Gly Tyr Trp Gln Gln Glu Ile Tyr Thr Val
Asn Ser Asn 100 105 110 Phe Gly Thr Ser Asp Asp Leu Leu Ala Leu Ser
Lys Ala Leu His Asp 115 120 125 Arg Gly Met Tyr Leu Met Val Asp Val
Val Ala Asn His Met Gly Tyr 130 135 140 Asp Gly Asp Gly Asp Ser Val
Asp Tyr Ser Val Phe Asn Pro Phe Asn 145 150 155 160 Ser Ser Ser Tyr
Phe His Pro Tyr Cys Leu Ile Thr Asp Tyr Ser Asn 165 170 175 Gln Thr
Asp Val Glu Asp Cys Trp Leu Gly Asp Thr Thr Val Ser Leu 180 185 190
Pro Asp Leu Asn Thr Thr Glu Thr Val Val Arg Thr Ile Trp Tyr Asp 195
200 205 Trp Val Ala Asp Leu Val Ser Asn Tyr Ser Ile Asp Gly Leu Arg
Ile 210 215 220 Asp Thr Val Lys His Val Glu Lys Ser Phe Trp Pro Gly
Tyr Asn Ser 225 230 235 240 Ala Ala Gly Val Tyr Cys Val Gly Glu Val
Leu Asp Gly Asp Pro Ser 245 250 255 Tyr Thr Cys Pro Tyr Gln Asp Tyr
Leu Asp Gly Val Leu Asn Tyr Pro 260 265 270 Ile Tyr Tyr Gln Leu Leu
Tyr Ala Phe Glu Ser Ser Ser Gly Ser Ile 275 280 285 Ser Asn Leu Tyr
Asn Met Ile Asn Ser Val Ala Ser Glu Cys Ser Asp 290 295 300 Pro Thr
Leu Leu Gly Asn Phe Ile Glu Asn His Asp Asn Pro Arg Phe 305 310 315
320 Ala Ser Tyr Thr Ser Asp Tyr Ser Leu Ala Lys Asn Val Ile Ala Phe
325 330 335 Ile Phe Phe Ser Asp Gly Ile Pro Ile Val Tyr Ala Gly Gln
Glu Gln 340 345 350 His Tyr Asn Gly Gly Asn Asp Pro Tyr Asn Arg Glu
Ala Thr Trp Leu 355 360 365 Ser Gly Tyr Ser Thr Thr Ala Glu Leu Tyr
Thr Phe Ile Ala Thr Thr 370 375 380 Asn Ala Ile Arg Ser Leu Ala Ile
Ser Val Asp Ser Glu Tyr Leu Thr 385 390 395 400 Tyr Lys Asn Asp Pro
Phe Tyr Tyr Asp Ser Asn Thr Leu Ala Met Arg 405 410 415 Lys Gly Ser
Asp Gly Leu Gln Val Ile Thr Val Leu Ser Asn Leu Gly 420 425 430 Ala
Asp Gly Ser Ser Tyr Thr Leu Thr Leu Ser Gly Ser Gly Tyr Ser 435 440
445 Ser Gly Thr Glu Leu Val Glu Ala Tyr Thr Cys Thr Thr Val Thr Val
450 455 460 Asp Ser Asn Gly Asp Ile Pro Val Pro Met Glu Ser Gly Leu
Pro Arg 465 470 475 480 Val Phe Leu Pro Ala Ser Ser Phe Ser Gly Ser
Ser Leu Cys Ser Ser 485 490 495 Ser Pro Ser Pro Thr Thr Thr Thr Ser
Thr Ser Thr Ser Thr Thr Ser 500 505 510 Thr Ala Cys Thr Thr Ala Thr
Ala Val Ala Val Leu Phe Glu Glu Leu 515 520 525 Val Thr Thr Thr Tyr
Gly Glu Asn Val Tyr Leu Ser Gly Ser Ile Ser 530 535 540 Gln Leu Gly
Asp Trp Asn Thr Asp Asp Ala Val Ala Leu Ser Ala Ala 545 550 555 560
Asn Tyr Thr Ser Ser Asn Pro Leu Trp Tyr Val Thr Val Thr Leu Pro 565
570 575 Val Gly Thr Ser Phe Glu Tyr Lys Phe Ile Lys Lys Glu Glu Asn
Gly 580 585 590 Asp Val Glu Trp Glu Ser Asp Pro Asn Arg Ser Tyr Thr
Val Pro Thr 595 600 605 Ala Cys Thr Gly Ala Thr Glu Thr Ile Val Asp
Thr Trp Arg 610 615 620 2618PRTRasamsonia emersonii 2Met Ala Ser
Leu Val Ala Gly Ala Leu Cys Ile Leu Gly Leu Thr Pro 1 5 10 15 Ala
Ala Phe Ala Arg Ala Pro Val Ala Ala Arg Ala Thr Gly Ser Leu 20 25
30 Asp Ser Phe Leu Ala Thr Glu Thr Pro Ile Ala Leu Gln Gly Val Leu
35 40 45 Asn Asn Ile Gly Pro Asn Gly Ala Asp Val Ala Gly Ala Ser
Ala Gly 50 55 60 Ile Val Val Ala Ser Pro Ser Arg Ser Asp Pro Asn
Tyr Phe Tyr Ser 65 70 75 80 Trp Thr Arg Asp Ala Ala Leu Thr Ala Lys
Tyr Leu Val Asp Ala Phe 85 90 95 Ile Ala Gly Asn Lys Asp Leu Glu
Gln Thr Ile Gln Gln Tyr Ile Ser 100 105 110 Ala Gln Ala Lys Val Gln
Thr Ile Ser Asn Pro Ser Gly Asp Leu Ser 115 120 125 Thr Gly Gly Leu
Gly Glu Pro Lys Phe Asn Val Asn Glu Thr Ala Phe 130 135 140 Thr Gly
Pro Trp Gly Arg Pro Gln Arg Asp Gly Pro Ala Leu Arg Ala 145 150 155
160 Thr Ala Leu Ile Ala Tyr Ala Asn Tyr Leu Ile Asp Asn Gly Glu Ala
165 170 175 Ser Thr Ala Asp Glu Ile Ile Trp Pro Ile Val Gln Asn Asp
Leu Ser 180 185 190 Tyr Ile Thr Gln Tyr Trp Asn Ser Ser Thr Phe Asp
Leu Trp Glu Glu 195 200 205 Val Glu Gly Ser Ser Phe Phe Thr Thr Ala
Val Gln His Arg Ala Leu 210 215 220 Val Glu Gly Asn Ala Leu Ala Thr
Arg Leu Asn His Thr Cys Ser Asn 225 230 235 240 Cys Val Ser Gln Ala
Pro Gln Val Leu Cys Phe Leu Gln Ser Tyr Trp 245 250 255 Thr Gly Ser
Tyr Val Leu Ala Asn Phe Gly Gly Ser Gly Arg Ser Gly 260 265 270 Lys
Asp Val Asn Ser Ile Leu Gly Ser Ile His Thr Phe Asp Pro Ala 275 280
285 Gly Gly Cys Asp Asp Ser Thr Phe Gln Pro Cys Ser Ala Arg Ala Leu
290 295 300 Ala Asn His Lys Val Val Thr Asp Ser Phe Arg Ser Ile Tyr
Ala Ile 305 310 315 320 Asn Ser Gly Ile Ala Glu Gly Ser Ala Val Ala
Val Gly Arg Tyr Pro 325 330 335 Glu Asp Val Tyr Gln Gly Gly Asn Pro
Trp Tyr Leu Ala Thr Ala Ala 340 345 350 Ala Ala Glu Gln Leu Tyr Asp
Ala Ile Tyr Gln Trp Lys Lys Ile Gly 355 360 365 Ser Ile Ser Ile Thr
Asp Val Ser Leu Pro Phe Phe Gln Asp Ile Tyr 370 375 380 Pro Ser Ala
Ala Val Gly Thr Tyr Asn Ser Gly Ser Thr Thr Phe Asn 385 390 395 400
Asp Ile Ile Ser Ala Val Gln Thr Tyr Gly Asp Gly Tyr Leu Ser Ile 405
410 415 Val Glu Lys Tyr Thr Pro Ser Asp Gly Ser Leu Thr Glu Gln Phe
Ser 420 425 430 Arg Thr Asp Gly Thr Pro Leu Ser Ala Ser Ala Leu Thr
Trp Ser Tyr 435 440 445 Ala Ser Leu Leu Thr Ala Ser Ala Arg Arg Gln
Ser Val Val Pro Ala 450 455 460 Ser Trp Gly Glu Ser Ser Ala Ser Ser
Val Pro Ala Val Cys Ser Ala 465 470 475 480 Thr Ser Ala Thr Gly Pro
Tyr Ser Thr Ala Thr Asn Thr Val Trp Pro 485 490 495 Ser Ser Gly Ser
Gly Ser Ser Thr Thr Thr Ser Ser Ala Pro Cys Thr 500 505 510 Thr Pro
Thr Ser Val Ala Val Thr Phe Asp Glu Ile Val Ser Thr Ser 515 520 525
Tyr Gly Glu Thr Ile Tyr Leu Ala Gly Ser Ile Pro Glu Leu Gly Asn 530
535 540 Trp Ser Thr Ala Ser Ala Ile Pro Leu Arg Ala Asp Ala Tyr Thr
Asn 545 550 555 560 Ser Asn Pro Leu Trp Tyr Val Thr Val Asn Leu Pro
Pro Gly Thr Ser 565 570 575 Phe Glu Tyr Lys Phe Phe Lys Asn Gln Thr
Asp Gly Thr Ile Val Trp 580 585 590 Glu Asp Asp Pro Asn Arg Ser Tyr
Thr Val Pro Ala Tyr Cys Gly Gln 595 600 605 Thr Thr Ala Ile Leu Asp
Asp Ser Trp Gln 610 615 31869DNAArtificial SequenceSynthetic DNA
sequence coding for Rasamsonia emersonii alpha-amylase 3atgacgcctt
tcgtcctcac ggccgtgctg ttcttgctgg ggaatgccgt gttggccttg 60accccggccg
aatggcgcaa acaatctatc tactttctcc tcacggaccg ctttggcagg
120gcagataact cgaccactgc tgcctgcgat gtcactgaga ggatctactg
tggcgggagt 180tggcaaggaa tcatcaacca tctcgactat atccaaggca
tggggttcac ggccatctgg 240atttcaccgg tgaccgagca gctgccgcaa
aatacgggtg agggagaagc ctatcatggg 300tattggcagc aggaaatata
cacggtcaac tccaactttg ggacatcaga cgatctctta 360gccctgtcaa
aggcgctcca tgaccgtggc atgtacctca tggtcgatgt ggttgcgaat
420cacatgggat acgatggaga tggcgactcc gttgattaca gcgtcttcaa
tccatttaat 480tcctctagtt atttccatcc ctattgcctg attacagact
acagcaatca gaccgatgtg 540gaagactgtt ggctgggcga tacgactgtc
tcgttgcccg atctcaacac cacggagact 600gttgtgagga ctatatggta
tgactgggtg gcggatctcg tctccaatta ctctattgat 660gggcttcgca
tcgacacggt gaaacacgta gaaaagtcat tctggcctgg ttacaacagt
720gctgcgggtg tctactgtgt tggcgaggtc ctcgatggag atccgtctta
cacttgtccc 780taccaggatt atctggacgg tgtattaaac tatccaatat
actatcaact actgtatgcg 840tttgaatcct ctagcggcag catcagcaat
ctttacaaca tgatcaactc tgtcgcctct 900gaatgttccg atcccactct
gttgggcaac tttatcgaga accatgacaa ccctagattt 960gcctcctata
caagtgatta ttctcttgct aaaaatgtga ttgctttcat cttcttctct
1020gacggcatcc ctatcgtcta tgccggtcag gagcagcatt acaacggggg
aaatgacccc 1080tacaaccgcg aggccacctg gctgtcagga tactcgacga
cggccgaact gtacacgttc 1140attgcgacca ccaacgcgat ccgtagcttg
gcgatctccg tcgactcgga gtatttgacg 1200tacaagaatg acccattcta
ctacgacagc aataccctcg ctatgcgcaa gggttcggat 1260ggcctgcagg
tcatcactgt tctgtccaat ctgggcgccg atggtagctc gtacacgttg
1320actctgagtg gcagtggcta ttcgtcaggc acggagctgg tggaagctta
cacctgcaca 1380acggtcactg ttgactctaa tggcgatatt ccagttccca
tggagtccgg actgccgcgc 1440gttttcctac cagcatcctc attcagtggt
agcagtctat gcagttcttc tcctagccct 1500actactacaa catcgacatc
gacatcgaca acgtcgacgg cctgcaccac cgccaccgct 1560gtggcggtcc
tcttcgaaga gttggtgaca acgacctacg gtgaaaatgt ctacctcagc
1620ggatcgatca gccaactcgg ggactggaac acggacgacg ccgtggccct
gtccgcagct 1680aattacactt cttcgaatcc cctgtggtat gtgacagtca
cattgccggt tgggacgtcc 1740tttgagtaca agttcatcaa gaaggaagag
aacggcgatg tcgagtggga gagcgatccc 1800aatcggtcgt atactgtgcc
gacggcctgc acgggagcga cggagacgat tgtcgacaca 1860tggagatag
186941854DNAArtificial SequenceOptimised DNA sequence coding for
the Rasamsonia emersonii glucoamylase 4atggcctcct tagtcgcagg
tgccttatgt attttaggtt tgaccccagc agccttcgca 60agagccccag tcgcagccag
agcaacaggt tcattggatt catttttggc tacagaaact 120ccaatcgcat
tgcaaggtgt tttgaacaac atcggtccaa acggtgctga tgttgctggt
180gcatctgctg gtattgttgt tgcatctcca tctagatcag atccaaacta
cttctactct 240tggactagag atgctgcatt gactgctaag tatttggttg
atgcttttat tgcaggtaat 300aaggatttgg aacaaactat ccaacaatac
atctctgcac aagctaaggt tcaaactatc 360tcaaacccat ctggtgactt
gtctacaggt ggtttgggtg aaccaaagtt taatgttaac 420gaaactgctt
ttacaggtcc atggggtaga ccacaaagag atggtccagc attgagagca
480actgctttga tcgcatacgc taactacttg atcgataacg gtgaagcttc
tacagcagat 540gaaatcatct ggccaatcgt tcaaaacgat ttgtcataca
tcactcaata ctggaactct 600tctacatttg atttgtggga agaagttgaa
ggttcttctt tctttactac agctgttcaa 660catagagcat tagttgaggg
taatgcattg gctactagat tgaaccatac atgttcaaac 720tgtgtttctc
aagctccaca agtcttgtgt ttcttgcaat catattggac tggttcttac
780gttttggcta attttggtgg ttcaggtaga tcaggtaaag atgttaattc
aatcttgggt 840tctattcata cttttgatcc agctggtggt tgtgatgatt
ctacatttca accatgttca 900gcaagagctt tggcaaacca taaggttgtt
actgattctt ttagatcaat ctatgctatt 960aattctggta ttgcagaagg
ttcagctgtt gcagttggta gatatccaga agatgtttac 1020caaggtggta
atccatggta cttggctact gctgcagctg cagaacaatt gtacgatgca
1080atctatcaat ggaagaaaat tggttcaatc tctatcacag atgtttcttt
gccatttttc 1140caagatatct atccatcagc tgcagttggt acttacaact
caggttctac tacttttaat 1200gatatcattt ctgctgttca aacatatggt
gacggttact tgtcaatcgt tgaaaagtac 1260actccatcag atggttcttt
gacagaacaa ttttctagaa ctgatggtac accattgtca 1320gcttctgcat
taacttggtc atacgcttct ttgttaacag cttcagcaag aagacaatct
1380gttgttccag catcatgggg tgaatcttca gcttcttcag ttccagcagt
ttgttcagct 1440acttctgcaa caggtccata ttctacagct actaatacag
tttggccatc ttcaggttca 1500ggttcttcaa ctacaacttc ttcagctcca
tgtacaactc caacttctgt tgcagttaca 1560ttcgatgaaa tcgtttcaac
ttcttacggt gaaacaatat atttggctgg ttctattcca 1620gaattgggta
attggtcaac tgcttctgca attccattga gagctgatgc atacacaaat
1680tctaatccat tgtggtatgt tactgttaat ttgccaccag gtacatcatt
cgaatacaag 1740tttttcaaga atcaaactga tggtacaatt gtttgggaag
atgatccaaa tagatcctac 1800accgttcctg cttactgtgg tcaaactacc
gcaatcttgg acgactcttg gcaa 185451857DNAArtificial SequenceAdapted
native DNA sequence coding for Rasamsonia emersonii glucoamylase
5atggcgtccc tcgttgctgg cgctctctgc atcctgggcc tgacgcctgc tgcatttgca
60cgagcgcccg ttgcagcgcg agccaccggt tccctggact cctttctcgc aaccgaaact
120ccaattgccc tccaaggcgt gctgaacaac atcgggccca atggtgctga
tgtggcagga 180gcaagcgccg gcattgtggt tgccagtccg agcaggagcg
acccaaatta tttctactcc 240tggacacgtg acgcagcgct cacggccaaa
tacctcgttg acgccttcat cgcgggcaac 300aaggacctag agcagaccat
ccagcagtac atcagcgcgc aggcgaaggt gcaaactatc 360tccaatccgt
ccggagattt atccaccggt ggcttaggtg agcccaagtt caatgtgaat
420gagacggctt ttaccgggcc ctggggtcgt ccacagaggg acggaccagc
gttgagagcg 480acggccctca ttgcgtatgc gaactatctc atcgacaacg
gcgaggcttc gactgccgat 540gagatcatct ggccgattgt ccagaatgat
ctgtcctaca tcacccaata ctggaactca 600tccaccttcg acctctggga
agaagtagaa ggttcctcat tcttcacaac cgccgtgcaa 660caccgcgccc
tggtcgaagg caatgcactg gcaacaaggc tgaaccacac gtgctccaac
720tgcgtctctc aggcccctca ggtcctgtgt ttcctgcagt catactggac
cggatcgtat 780gttctggcca actttggtgg cagcggtcgt tccggcaagg
acgtgaactc gattctgggc 840agcatccaca cctttgatcc cgccggaggc
tgtgacgact cgaccttcca gccgtgttcg 900gcccgtgcct tggcaaatca
caaggtggtc accgactcgt tccggagtat ctatgcgatc 960aactcaggca
tcgcagaggg atctgccgtg gcagtcggcc gctaccctga ggatgtctac
1020cagggcggga acccctggta cctggccaca gcagcggctg cagagcagct
ttacgacgcc 1080atctaccagt ggaagaagat cggctcgata agtatcacgg
acgttagtct gccatttttc 1140caggatatct acccttctgc cgcggtgggc
acctataact ctggctccac gactttcaac 1200gacatcatct cggccgtcca
gacgtatggt gatggatatc tgagtattgt cgagaaatat 1260actccctcag
acggctctct taccgaacaa ttctcccgta cagacggcac tccgctttct
1320gcctctgccc tgacttggtc gtacgcttct ctcctaaccg cttcggcccg
cagacagtcc 1380gtcgtccctg cttcctgggg cgaaagctcc gcaagcagcg
tccctgccgt ctgctctgcc 1440acctctgcca cgggcccata cagcacggct
accaacaccg tctggccaag ctctggctct 1500ggcagctcaa caaccaccag
tagcgcccca tgcaccactc ctacctctgt ggctgtgacc 1560ttcgacgaaa
tcgtcagcac cagttacggg gagacaatct acctggccgg ctcgatcccc
1620gagctgggca actggtccac ggccagcgcg atccccctcc gcgcggatgc
ttacaccaac 1680agcaacccgc tctggtacgt gaccgtcaat ctgccccctg
gcaccagctt cgagtacaag 1740ttcttcaaga accagacgga cgggaccatc
gtctgggaag acgacccgaa ccggtcgtac 1800acggtcccag cgtactgtgg
gcagactacc gccattcttg acgatagttg gcagtga 185761869DNARasamsonia
emersonii 6atgacgcctt tcgtcctcac ggccgtgctg ttcttgctgg ggaatgccgt
gttggccttg 60accccggccg aatggcgcaa acaatctatc tactttctcc tcacggaccg
ctttggcagg 120gcagataact cgaccactgc tgcctgcgat gtcactgaga
ggatctactg tggcgggagt 180tggcaaggaa tcatcaacca tctcgactat
atccaaggca tggggttcac ggccatctgg 240atttcaccgg tgaccgagca
gctgccgcaa aatacgggtg agggagaagc ctatcatggg 300tattggcagc
aggaaatata cacggtcaac tccaactttg ggacatcaga cgatctctta
360gccctgtcaa aggcgctcca tgaccgtggc atgtacctca tggtcgatgt
ggttgcgaat 420cacatgggat acgatggaga tggcgactcc gttgattaca
gcgtcttcaa tccatttaat 480tcctcgagtt atttccatcc ctattgcctg
attacagact acagcaatca gaccgatgtg 540gaagactgtt ggctgggcga
tacgactgtc tcgttgcccg atctcaacac cacggagact 600gttgtgagga
ctatatggta tgactgggtg gcggatctcg tctccaatta ctctattgat
660gggcttcgca tcgacacggt gaaacacgta gaaaagtcat tctggcctgg
ttacaacagt 720gctgcgggtg tctactgtgt tggcgaggtc ctcgatggag
atccgtctta cacttgtccc 780taccaggatt atctggacgg tgtattaaac
tatccaatat actatcaact actgtatgcg 840tttgaatcct ctagcggcag
catcagcaat ctttacaaca tgatcaactc tgtcgcctct 900gaatgttccg
atcccactct gttgggcaac tttatcgaga accatgacaa ccctagattt
960gcctcctata caagtgatta ttctcttgct aaaaatgtga ttgctttcat
cttcttctct 1020gacggcatcc ctatcgtcta tgccggtcag gagcagcatt
acaacggggg aaatgacccc 1080tacaaccgcg aggccacctg gctgtcagga
tactcgacga cggccgaact gtacacgttc 1140attgcgacca ccaacgcgat
ccgtagcttg gcgatctccg tcgactcgga gtatttgacg 1200tacaagaatg
acccattcta ctacgacagc aataccctcg ctatgcgcaa gggttcggat
1260ggcctgcagg tcatcactgt tctgtccaat ctgggcgccg atggtagctc
gtacacgttg 1320actctgagtg gcagtggcta ttcgtcaggc acggagctgg
tggaagctta cacctgcaca 1380acggtcactg ttgactctaa tggcgatatt
ccagttccca tggagtccgg actgccgcgc 1440gttttcctac cagcatcctc
attcagtggt agcagtctat gcagttcttc tcctagccct 1500actactacaa
catcgacatc gacatcgaca acgtcgacgg cctgcaccac cgccaccgct
1560gtggcggtcc tcttcgaaga gttggtgaca acgacctacg gtgaaaatgt
ctacctcagc 1620ggatcgatca gccaactcgg ggactggaac acggacgacg
ccgtggccct gtccgcagct 1680aattacactt cttcgaatcc cctgtggtat
gtgacagtca cattgccggt tgggacgtcc 1740tttgagtaca agttcatcaa
gaaggaagag aacggcgatg tcgagtggga gagcgatccc 1800aatcggtcgt
atactgtgcc gacggcctgc acgggagcga cggagacgat tgtcgacaca
1860tggagatag 186972748DNATalaromyces emersonii 7acgagatgtg
tatatactgt gaaccaaact agatgatgtc agttatgctg gtctgagaac 60tcatagaagc
ccttgaaaat accccaagct agcactccaa ccctaactct gttgctctac
120tagatcaaga cgagtactct gattgagctg caggcttgga atatatgatt
agcagaaaaa 180gggttaaaac ttgtatgaca atcagtttgt cagtactccg
tagtgatgcc atgtctatag 240agtcgacact aaggcagcat gtgaatgagt
cggaaatgac aggaagcaga ttccttaaca 300gtcatgttct ccgtgcctgc
atccccacgt cacctgcaaa gatgcgacgc tactccacac 360cggcgccttg
atgtctgctg ttcctggcct agtggagccc catgcgctgc tagctcgtgg
420tcttcgaata aatcagaata aaaaacggag taattaattg cgcccgcaac
aaactaagca 480atgtaactca atgccaagct tccgctgatg ctcttgacat
ctccgtagtg gcttctttcg 540taatttcaga cgtatatata gtagtaatgc
ccagcaggcc gggataatga tggggatttc 600tgaactctca gcttccgtac
gctgaacagt ttgcttgcgt tgtcaaccat ggcgtccctc 660gttgctggcg
ctctctgcat cctgggcctg acgcctgctg catttgcacg agcgcccgtt
720gcagcgcgag ccaccggttc cctggactcc tttctcgcaa ccgaaactcc
aattgccctc 780caaggcgtgc tgaacaacat cgggcccaat ggtgctgatg
tggcaggagc aagcgccggc 840attgtggttg ccagtccgag caggagcgac
ccaaattgta ggttctttcc caccagaaat 900tacttattta aatcagccct
ctgacaggtt gaagatttct actcctggac acgtgacgca 960gcgctcacgg
ccaaatacct cgtcgacgcc ttcatcgcgg gcaacaagga cctagagcag
1020accatccagc agtacatcag cgcgcaggcg aaggtgcaaa ctatctccaa
tccgtccgga 1080gatttatcca ccggtggctt aggtgagccc aagttcaatg
tgaatgagac ggcttttacc 1140gggccctggg gtcgtccaca gagggacgga
ccagcgttga gagcgacggc cctcattgcg 1200tatgcgaact atctcatcgt
aagcttctgc tcgctgccct tctctctgct cgtatgctaa 1260gtagtcctgt
caggacaacg gcgaggcttc gactgccgat gagatcatct ggccgattgt
1320ccagaatgat ctgtcctaca tcacccaata ctggaactca tccaccttcg
gtaggcaaat 1380gaatattccc gacacagcgt ggtactaatt tgattcagac
ctctgggaag aagtagaagg 1440atcctcattc ttcacaaccg ccgtgcaaca
ccgcgccctg gtcgaaggca atgcactggc 1500aacaaggctg aaccacacgt
gctccaactg cgtctctcag gcccctcagg tcctgtgttt 1560cctgcagtca
tactggaccg gatcgtatgt tctggccaac tttggtggca gcggtcgttc
1620cggcaaggac gtgaattcga ttctgggcag catccacacc tttgatcccg
ccggaggctg 1680tgacgactcg accttccagc cgtgttcggc ccgtgccttg
gcaaatcaca aggtggtcac 1740cgactcgttc cggagtatct atgcgatcaa
ctcaggcatc gcagagggat ctgccgtggc 1800agtcggccgc taccctgagg
atgtctacca gggcgggaac ccctggtacc tggccacagc 1860agcggctgca
gagcagcttt acgacgccat ctaccagtgg aagaagatcg gctcgataag
1920tatcacggac gttagtctgc catttttcca ggatatctac ccttctgccg
cggtgggcac 1980ctataactct ggctccacga ctttcaacga catcatctcg
gccgtccaga cgtatggtga 2040tggatatctg agtattgtcg tacgttttgc
cttagattct caggtgtaaa gaaaaaaatg 2100gaactaactc agttctagga
gaaatatact ccctcagacg gctctcttac cgaacaattc 2160tcccgtacag
acggcactcc gctttctgcc tctgccctga cttggtcgta cgcttctctc
2220ctaaccgctt cggcccgcag acagtccgtc gtccctgctt cctggggcga
aagctccgca 2280agcagcgtcc ctgccgtctg ctctgccacc tctgccacgg
gcccatacag cacggctacc 2340aacaccgtct ggccaagctc tggctctggc
agctcaacaa ccaccagtag cgccccatgc 2400accactccta cctctgtggc
tgtgaccttc gacgaaatcg tcagcaccag ttacggggag 2460acaatctacc
tggccggctc gatccccgag ctgggcaact ggtccacggc cagcgcgatc
2520cccctccgcg cggatgctta caccaacagc aacccgctct ggtacgtgac
cgtcaatctg 2580ccccctggca ccagcttcga gtacaagttc ttcaagaacc
agacggacgg gaccatcgtc 2640tgggaagacg acccgaaccg gtcgtacacg
gtcccagcgt actgtgggca gactaccgcc 2700attcttgacg atagttggca
gtgagataac atccaccctt ctgtttta 2748866DNAArtificial SequencePCR
oligo-primer for ApuA_Nat-L 8tgcttatcaa cacacaaaca ctaaatcaaa
gaattcatgg cagccaacta cgtttctcga 60ttgttg 66960DNAArtificial
SequencePCR oligo-primer for ApuA_N-R 9gactagaagg cttaatcaaa
agctctcgag tcacccctgc caagtattgc tgaccgatgc 601060DNAArtificial
SequencePCR oligo-primer for ApuA_Opt-NatSS-L 10tctctacttg
accgggttgg tgcagtgttt gactccagct caatggagaa gtcaatctat
601160DNAArtificial SequencePCR oligo-primer for ApuA_Opt-R
11ggactagaag gcttaatcaa aagctctcga gctaaccttg ccatgtattg gagactgagg
601255DNAArtificial SequencePCR oligo-primer for ApuA_optXynSec-L
12gaacccgtgg ctgtggagaa gcgctcgcga ttgactccag ctcaatggag aagtc
551360DNAArtificial SequencePCR oligo-primer for ApuA_Opt-R
13ggactagaag gcttaatcaa aagctctcga gctaaccttg ccatgtattg gagactgagg
601466DNAArtificial SequencePCR oligo-primer for AteA_Nat-L
14tgcttatcaa cacacaaaca ctaaatcaaa gaattcatga agtggacctc ctcgctcctc
60ctctta 661560DNAArtificial SequencePCR oligo-primer for
AteA_Nat-R 15gactagaagg cttaatcaaa agctctcgag tcacctccaa gtatcagcaa
ctgtcaccgt 601660DNAArtificial SequencePCR oligo-primer for
TemA_Nat-L 16tgcttatcaa cacacaaaca ctaaatcaaa gaattcatga cgcctttcgt
cctcacggcc 601760DNAArtificial SequencePCR oligo-primer for
TemA_Nat-R 17ggactagaag gcttaatcaa aagctctcga gctatctcca tgtgtcgaca
atcgtctccg 601860DNAArtificial SequencePCR oligo-primer for
TemA_Opt-NatOptSS-L 18tgcttatcaa cacacaaaca ctaaatcaaa gaattcatga
ccccttttgt tttgacagcc 601960DNAArtificial SequencePCR oligo-primer
for TemA_Opt-R 19ggactagaag gcttaatcaa aagctctcga gctatctcca
agtgtcaaca atagtttcag 602058DNAArtificial SequencePCR oligo-primer
for TemA_Nat-xynsecSS-L 20gaacccgtgg ctgtggagaa gcgctcgcga
ttgaccccgg ccgaatggcg caaacaat 582159DNAArtificial SequencePCR
oligo-primer for TemA_Opt-xynsecSS-L 21gaacccgtgg ctgtggagaa
gcgctcgcga ttgacaccag ccgaatggag aaagcaatc 592251DNAArtificial
SequencePCR oligo-primer for TemA_Opt-NatSS-L 22tcttgctggg
gaatgccgtg ttggccttga caccagccga atggagaaag c 512366DNAArtificial
SequencePCR oligo-primer for AteG_Nat-L 23tgcttatcaa cacacaaaca
ctaaatcaaa gaattcatga cgcgcattct caccctcgcc 60cttcat
662461DNAArtificial SequencePCR oligo-primer for AteG_Nat-R
24ggactagaag gcttaatcaa aagctctcga gctagcgcca agtggtgttc accaccgcgg
60t 612560DNAArtificial SequencePCR oligo-primer for
AteG_Opt-NatSS-L 25gggctggctc ttgtccaaag tgttgttggg gcaccacaat
tggctcctag agcaactaca 602660DNAArtificial SequencePCR oligo-primer
for AteG_Opt-R 26tggactagaa ggcttaatca aaagctctcg agctatctcc
aggttgtgtt gacaacggcg 602760DNAArtificial SequencePCR oligo-primer
for AteG_Nat-xynSS-L 27gaacccgtgg ctgtggagaa gcgctcgcga gctccccaat
tggcccccag agcgacaacc 602866DNAArtificial SequencePCR oligo-primer
for TemG_Nat-L 28tgcttatcaa cacacaaaca ctaaatcaaa gaattcatgg
cgtccctcgt tgctggcgct 60ctctgc 662961DNAArtificial SequencePCR
oligo-primer for TemG_Nat-R 29ggactagaag gcttaatcaa aagctctcga
gtcactgcca actatcgtca agaatggcgg 60t 613060DNAArtificial
SequencePCR oligo-primer for TemG_Nat-xynsecSS-L 30gaacccgtgg
ctgtggagaa gcgctcgcga cgagcgcccg ttgcagcgcg agccaccggt
603160DNAArtificial SequencePCR oligo-primer for
TemG_Opt-xynsecSS-L 31gaacccgtgg ctgtggagaa gcgctcgcga agagccccag
tcgcagccag agcaacaggt 603260DNAArtificial SequencePCR oligo-primer
for TemG_Opt-R 32gactagaagg cttaatcaaa agctctcgag tcattgccaa
gagtcgtcca agattgcggt 603360DNAArtificial SequencePCR oligo-primer
for TemG_Opt-NatOptSS-L 33ttatcaacac acaaacacta aatcaaagaa
ttcatggcct ccttagtcgc aggtgcctta 603460DNAArtificial SequencePCR
oligo-primer for TemG_Opt-NatSS-L 34atcctgggcc tgacgcctgc
tgcatttgca agagccccag tcgcagccag agcaacaggt 603558DNAArtificial
SequencePCR oligo-primer ENOCASS-L 35gtgcggtatt tcacaccgca
taggagatcg atcccaatta atgtgagtta cctcactc 583635DNAArtificial
SequencePCR oligo-primer ENOCASS-R 36cgggcctctt cgctattacg
ccagagctta gatct 353762DNAArtificial SequencePCR primer amdSYMCas-L
37ccgcgcgttg gccgattcat taatccagga tccacatgga ggcccagaat accctccttg
60ac 623864DNAArtificial SequencePCR primer amdSYMCas-R
38gggcctcttc gctattacgc cagagcttag atctcagtat agcgaccagc attcacatac
60ttaa 6439128DNAArtificial SequencePCR primer Delta-ENO1p-L
39tggaataaaa atccactatc gtctatcaac taatagttat attatcaata tattatcata
60tacggtgtta agatgatgac ataagttatg agaagctgtc ggatcccaat taatgtgagt
120tacctcac 12840128DNAArtificial SequencePCR primer Delta-ENO1t-R
40tgagatatat gtgggtaatt agataattgt tgggattcca ttgttgataa aggctataat
60attaggtata cagaatatac tagaagttct cctcgaggat agatctccta tgcggtgtga
120aataccgc 1284160DNAArtificial SequencePCR primer TemG_Opt-L
41ttatcaacac acaaacacta aatcaaagaa ttcatggcct ccttagtcgc aggtgcctta
604260DNAArtificial SequencePCR primer TemG_Opt-R 42gactagaagg
cttaatcaaa agctctcgag tcattgccaa gagtcgtcca agattgcggt
604360DNAArtificial SequencePCR primer TemA_Nat-L 43tgcttatcaa
cacacaaaca ctaaatcaaa gaattcatga cgcctttcgt cctcacggcc
604460DNAArtificial SequencePCR primer TemA_Nat-R 44ggactagaag
gcttaatcaa aagctctcga gctatctcca tgtgtcgaca atcgtctccg
604521DNAArtificial SequencePCR primer URA3-L 45cgtggatgat
gtggtctcta c 214622DNAArtificial SequencePCR primer URA3-R
46gttcaccctc taccttagca tc 224722DNAArtificial SequencePCR primer
temA_Nat-L 47gcgatgtcac tgagaggatc ta 224820DNAArtificial
SequencetemA_Nat-R 48gaaatccaga tggccgtgaa 204920DNAArtificial
SequencePCR primer temG_Opt-L 49tacaggtggt ttgggtgaac
205021DNAArtificial SequencePCR primer temG_Opt-R 50ctctcaatgc
tggaccatct c 21
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References